Starting phenix.real_space_refine on Tue Sep 15 15:35:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rax_4786/09_2026/6rax_4786.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rax_4786/09_2026/6rax_4786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rax_4786/09_2026/6rax_4786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rax_4786/09_2026/6rax_4786.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rax_4786/09_2026/6rax_4786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rax_4786/09_2026/6rax_4786.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rax_4786/09_2026/6rax_4786.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rax_4786/09_2026/6rax_4786.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 44 5.49 5 S 239 5.16 5 C 25619 2.51 5 N 7193 2.21 5 O 7875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 340 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40970 Number of models: 1 Model: "" Number of chains: 19 Chain: "2" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4788 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 28, 'TRANS': 576} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "3" Number of atoms: 4879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4879 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 22, 'TRANS': 602} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "4" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5013 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 26, 'TRANS': 599} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "5" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4864 Classifications: {'peptide': 620} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 592} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "6" Number of atoms: 4986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4986 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 608} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "7" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4964 Classifications: {'peptide': 636} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 611} Unresolved chain links: 5 Chain breaks: 2 Unresolved chain link angles: 18 Unresolved chain link dihedrals: 19 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "X" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 424 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "Y" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4575 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 14, 'TRANS': 552} Chain: "H" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1583 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 9, 'TRANS': 185} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1498 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 14, 'TRANS': 170} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1381 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1677 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ILE%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.16, per 1000 atoms: 0.20 Number of scatterers: 40970 At special positions: 0 Unit cell: (214.92, 182.52, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 239 16.00 P 44 15.00 O 7875 8.00 N 7193 7.00 C 25619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 5 192 " - pdb=" SG CYS 5 202 " distance=2.06 Simple disulfide: pdb=" SG CYS 6 152 " - pdb=" SG CYS 6 179 " distance=2.04 Simple disulfide: pdb=" SG CYS 7 187 " - pdb=" SG CYS 7 211 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM40909 O3A ATP 5 801 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.8 seconds 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9610 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 35 sheets defined 36.3% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain '2' and resid 178 through 189 removed outlier: 3.732A pdb=" N ASN 2 182 " --> pdb=" O THR 2 178 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG 2 189 " --> pdb=" O GLN 2 185 " (cutoff:3.500A) Processing helix chain '2' and resid 198 through 211 removed outlier: 4.757A pdb=" N ILE 2 204 " --> pdb=" O TYR 2 200 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG 2 205 " --> pdb=" O ARG 2 201 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 226 Processing helix chain '2' and resid 236 through 256 removed outlier: 3.947A pdb=" N VAL 2 247 " --> pdb=" O ILE 2 243 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER 2 254 " --> pdb=" O ASP 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 257 through 260 Processing helix chain '2' and resid 283 through 287 removed outlier: 3.589A pdb=" N LEU 2 287 " --> pdb=" O LYS 2 284 " (cutoff:3.500A) Processing helix chain '2' and resid 455 through 460 removed outlier: 3.690A pdb=" N ILE 2 458 " --> pdb=" O ASP 2 455 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL 2 459 " --> pdb=" O PRO 2 456 " (cutoff:3.500A) Processing helix chain '2' and resid 462 through 466 Processing helix chain '2' and resid 473 through 484 removed outlier: 3.678A pdb=" N LYS 2 477 " --> pdb=" O HIS 2 473 " (cutoff:3.500A) Processing helix chain '2' and resid 516 through 525 removed outlier: 4.438A pdb=" N TYR 2 520 " --> pdb=" O GLN 2 516 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR 2 521 " --> pdb=" O PHE 2 517 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU 2 522 " --> pdb=" O LEU 2 518 " (cutoff:3.500A) Processing helix chain '2' and resid 550 through 554 removed outlier: 3.906A pdb=" N TRP 2 554 " --> pdb=" O SER 2 551 " (cutoff:3.500A) Processing helix chain '2' and resid 578 through 583 removed outlier: 3.606A pdb=" N ARG 2 582 " --> pdb=" O ASN 2 578 " (cutoff:3.500A) Processing helix chain '2' and resid 635 through 639 removed outlier: 3.739A pdb=" N ILE 2 638 " --> pdb=" O SER 2 635 " (cutoff:3.500A) Processing helix chain '2' and resid 653 through 668 Processing helix chain '2' and resid 693 through 707 removed outlier: 4.163A pdb=" N LEU 2 697 " --> pdb=" O PRO 2 693 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG 2 698 " --> pdb=" O GLN 2 694 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN 2 699 " --> pdb=" O ASP 2 695 " (cutoff:3.500A) Processing helix chain '2' and resid 718 through 731 removed outlier: 3.697A pdb=" N LYS 2 722 " --> pdb=" O ASP 2 718 " (cutoff:3.500A) Processing helix chain '2' and resid 742 through 759 removed outlier: 3.728A pdb=" N ILE 2 748 " --> pdb=" O ILE 2 744 " (cutoff:3.500A) Processing helix chain '2' and resid 764 through 782 removed outlier: 4.551A pdb=" N VAL 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE 2 780 " --> pdb=" O LEU 2 776 " (cutoff:3.500A) Processing helix chain '2' and resid 788 through 795 Processing helix chain '3' and resid 7 through 18 removed outlier: 3.707A pdb=" N ASP 3 11 " --> pdb=" O GLN 3 7 " (cutoff:3.500A) Processing helix chain '3' and resid 47 through 53 removed outlier: 3.963A pdb=" N LEU 3 51 " --> pdb=" O ASN 3 47 " (cutoff:3.500A) Processing helix chain '3' and resid 55 through 60 Processing helix chain '3' and resid 68 through 85 Processing helix chain '3' and resid 86 through 89 Processing helix chain '3' and resid 109 through 113 removed outlier: 4.173A pdb=" N LEU 3 113 " --> pdb=" O PRO 3 110 " (cutoff:3.500A) Processing helix chain '3' and resid 201 through 205 removed outlier: 4.436A pdb=" N LYS 3 204 " --> pdb=" O MET 3 201 " (cutoff:3.500A) Processing helix chain '3' and resid 219 through 223 removed outlier: 3.915A pdb=" N VAL 3 223 " --> pdb=" O ASP 3 220 " (cutoff:3.500A) Processing helix chain '3' and resid 276 through 286 removed outlier: 4.189A pdb=" N LYS 3 286 " --> pdb=" O LYS 3 282 " (cutoff:3.500A) Processing helix chain '3' and resid 290 through 299 removed outlier: 4.062A pdb=" N LEU 3 298 " --> pdb=" O LEU 3 294 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA 3 299 " --> pdb=" O SER 3 295 " (cutoff:3.500A) Processing helix chain '3' and resid 309 through 317 removed outlier: 4.792A pdb=" N CYS 3 314 " --> pdb=" O GLN 3 310 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU 3 315 " --> pdb=" O ALA 3 311 " (cutoff:3.500A) Processing helix chain '3' and resid 345 through 349 removed outlier: 3.618A pdb=" N GLN 3 348 " --> pdb=" O ALA 3 345 " (cutoff:3.500A) Processing helix chain '3' and resid 393 through 397 Processing helix chain '3' and resid 412 through 424 removed outlier: 3.839A pdb=" N ALA 3 416 " --> pdb=" O ILE 3 412 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL 3 420 " --> pdb=" O ALA 3 416 " (cutoff:3.500A) Processing helix chain '3' and resid 469 through 474 removed outlier: 3.684A pdb=" N ARG 3 473 " --> pdb=" O SER 3 469 " (cutoff:3.500A) Processing helix chain '3' and resid 487 through 502 removed outlier: 4.373A pdb=" N MET 3 491 " --> pdb=" O ASP 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 559 through 565 Processing helix chain '3' and resid 579 through 595 removed outlier: 3.842A pdb=" N ALA 3 583 " --> pdb=" O GLN 3 579 " (cutoff:3.500A) Processing helix chain '3' and resid 600 through 604 Processing helix chain '3' and resid 610 through 626 removed outlier: 3.554A pdb=" N THR 3 614 " --> pdb=" O ARG 3 610 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG 3 626 " --> pdb=" O HIS 3 622 " (cutoff:3.500A) Processing helix chain '3' and resid 632 through 646 removed outlier: 4.225A pdb=" N LEU 3 642 " --> pdb=" O ALA 3 638 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL 3 643 " --> pdb=" O ALA 3 639 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 174 Processing helix chain '4' and resid 177 through 182 Processing helix chain '4' and resid 194 through 205 Processing helix chain '4' and resid 216 through 220 removed outlier: 3.600A pdb=" N LYS 4 219 " --> pdb=" O ALA 4 216 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR 4 220 " --> pdb=" O HIS 4 217 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 216 through 220' Processing helix chain '4' and resid 223 through 231 Processing helix chain '4' and resid 232 through 252 Proline residue: 4 238 - end of helix removed outlier: 3.647A pdb=" N ASP 4 241 " --> pdb=" O ILE 4 237 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE 4 249 " --> pdb=" O ASN 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 378 through 382 removed outlier: 3.607A pdb=" N VAL 4 382 " --> pdb=" O ASN 4 379 " (cutoff:3.500A) Processing helix chain '4' and resid 438 through 442 removed outlier: 3.987A pdb=" N HIS 4 441 " --> pdb=" O GLY 4 438 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE 4 442 " --> pdb=" O LYS 4 439 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 438 through 442' Processing helix chain '4' and resid 444 through 456 removed outlier: 3.617A pdb=" N LEU 4 450 " --> pdb=" O GLU 4 446 " (cutoff:3.500A) Processing helix chain '4' and resid 459 through 467 removed outlier: 3.901A pdb=" N LEU 4 464 " --> pdb=" O ILE 4 460 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA 4 465 " --> pdb=" O TYR 4 461 " (cutoff:3.500A) Processing helix chain '4' and resid 475 through 477 No H-bonds generated for 'chain '4' and resid 475 through 477' Processing helix chain '4' and resid 478 through 487 removed outlier: 3.586A pdb=" N LEU 4 484 " --> pdb=" O LYS 4 480 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN 4 485 " --> pdb=" O GLY 4 481 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 527 removed outlier: 3.641A pdb=" N ASN 4 527 " --> pdb=" O GLN 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 564 through 568 Processing helix chain '4' and resid 588 through 596 Processing helix chain '4' and resid 641 through 646 removed outlier: 4.088A pdb=" N PHE 4 646 " --> pdb=" O LEU 4 642 " (cutoff:3.500A) Processing helix chain '4' and resid 660 through 675 removed outlier: 4.133A pdb=" N LEU 4 664 " --> pdb=" O PHE 4 660 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL 4 669 " --> pdb=" O ALA 4 665 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR 4 672 " --> pdb=" O LEU 4 668 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 695 removed outlier: 4.210A pdb=" N TYR 4 692 " --> pdb=" O VAL 4 688 " (cutoff:3.500A) Processing helix chain '4' and resid 696 through 698 No H-bonds generated for 'chain '4' and resid 696 through 698' Processing helix chain '4' and resid 711 through 720 removed outlier: 6.787A pdb=" N VAL 4 717 " --> pdb=" O ILE 4 713 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ASP 4 718 " --> pdb=" O GLN 4 714 " (cutoff:3.500A) Processing helix chain '4' and resid 734 through 749 Processing helix chain '4' and resid 757 through 769 removed outlier: 4.000A pdb=" N GLU 4 761 " --> pdb=" O LEU 4 757 " (cutoff:3.500A) Processing helix chain '5' and resid 27 through 32 removed outlier: 3.854A pdb=" N LYS 5 32 " --> pdb=" O GLN 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 32 through 41 removed outlier: 4.316A pdb=" N ILE 5 38 " --> pdb=" O TYR 5 34 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG 5 39 " --> pdb=" O LYS 5 35 " (cutoff:3.500A) Processing helix chain '5' and resid 50 through 60 removed outlier: 4.001A pdb=" N ASN 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) Processing helix chain '5' and resid 71 through 76 Processing helix chain '5' and resid 79 through 84 Processing helix chain '5' and resid 86 through 107 removed outlier: 4.229A pdb=" N GLU 5 92 " --> pdb=" O THR 5 88 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU 5 95 " --> pdb=" O LEU 5 91 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE 5 105 " --> pdb=" O VAL 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 131 through 135 Processing helix chain '5' and resid 312 through 325 Processing helix chain '5' and resid 328 through 333 Processing helix chain '5' and resid 343 through 348 Processing helix chain '5' and resid 351 through 356 removed outlier: 3.824A pdb=" N PHE 5 355 " --> pdb=" O THR 5 351 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY 5 356 " --> pdb=" O CYS 5 352 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 351 through 356' Processing helix chain '5' and resid 383 through 394 removed outlier: 3.661A pdb=" N LEU 5 387 " --> pdb=" O ALA 5 383 " (cutoff:3.500A) Processing helix chain '5' and resid 452 through 462 removed outlier: 3.862A pdb=" N MET 5 459 " --> pdb=" O ILE 5 455 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU 5 460 " --> pdb=" O HIS 5 456 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN 5 461 " --> pdb=" O GLU 5 457 " (cutoff:3.500A) Processing helix chain '5' and resid 489 through 496 removed outlier: 3.594A pdb=" N ASP 5 493 " --> pdb=" O PHE 5 489 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP 5 494 " --> pdb=" O GLY 5 490 " (cutoff:3.500A) Processing helix chain '5' and resid 522 through 535 Processing helix chain '5' and resid 554 through 566 Processing helix chain '5' and resid 574 through 598 removed outlier: 3.704A pdb=" N GLY 5 578 " --> pdb=" O SER 5 574 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU 5 579 " --> pdb=" O GLU 5 575 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS 5 580 " --> pdb=" O ALA 5 576 " (cutoff:3.500A) Processing helix chain '5' and resid 608 through 627 removed outlier: 4.184A pdb=" N LEU 5 612 " --> pdb=" O THR 5 608 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG 5 617 " --> pdb=" O GLU 5 613 " (cutoff:3.500A) Processing helix chain '5' and resid 632 through 650 removed outlier: 3.502A pdb=" N VAL 5 636 " --> pdb=" O THR 5 632 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU 5 638 " --> pdb=" O GLU 5 634 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA 5 639 " --> pdb=" O HIS 5 635 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL 5 645 " --> pdb=" O ARG 5 641 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER 5 646 " --> pdb=" O LEU 5 642 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 31 removed outlier: 3.599A pdb=" N GLU 6 31 " --> pdb=" O ASP 6 27 " (cutoff:3.500A) Processing helix chain '6' and resid 41 through 49 removed outlier: 4.325A pdb=" N SER 6 49 " --> pdb=" O ALA 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 66 removed outlier: 3.869A pdb=" N GLU 6 63 " --> pdb=" O PHE 6 59 " (cutoff:3.500A) Processing helix chain '6' and resid 69 through 74 Processing helix chain '6' and resid 76 through 94 Proline residue: 6 82 - end of helix removed outlier: 3.701A pdb=" N CYS 6 85 " --> pdb=" O TYR 6 81 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP 6 94 " --> pdb=" O ASN 6 90 " (cutoff:3.500A) Processing helix chain '6' and resid 325 through 330 Processing helix chain '6' and resid 331 through 334 Processing helix chain '6' and resid 337 through 344 Processing helix chain '6' and resid 355 through 365 removed outlier: 5.381A pdb=" N LEU 6 361 " --> pdb=" O LYS 6 357 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU 6 362 " --> pdb=" O ARG 6 358 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN 6 363 " --> pdb=" O GLY 6 359 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN 6 364 " --> pdb=" O ILE 6 360 " (cutoff:3.500A) Processing helix chain '6' and resid 394 through 400 removed outlier: 4.115A pdb=" N LEU 6 398 " --> pdb=" O LYS 6 394 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN 6 400 " --> pdb=" O GLN 6 396 " (cutoff:3.500A) Processing helix chain '6' and resid 400 through 405 Processing helix chain '6' and resid 460 through 469 removed outlier: 4.037A pdb=" N GLU 6 467 " --> pdb=" O VAL 6 463 " (cutoff:3.500A) Processing helix chain '6' and resid 507 through 512 Processing helix chain '6' and resid 516 through 522 Processing helix chain '6' and resid 533 through 545 removed outlier: 3.613A pdb=" N ASP 6 537 " --> pdb=" O ASN 6 533 " (cutoff:3.500A) Processing helix chain '6' and resid 560 through 571 Processing helix chain '6' and resid 580 through 585 Processing helix chain '6' and resid 585 through 597 Processing helix chain '6' and resid 610 through 626 Processing helix chain '6' and resid 633 through 652 removed outlier: 3.690A pdb=" N VAL 6 637 " --> pdb=" O LEU 6 633 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 19 Processing helix chain '7' and resid 31 through 42 Processing helix chain '7' and resid 51 through 59 removed outlier: 3.722A pdb=" N LEU 7 55 " --> pdb=" O ASP 7 51 " (cutoff:3.500A) Processing helix chain '7' and resid 65 through 70 removed outlier: 4.330A pdb=" N ASN 7 69 " --> pdb=" O ALA 7 65 " (cutoff:3.500A) Processing helix chain '7' and resid 71 through 82 Processing helix chain '7' and resid 97 through 108 Processing helix chain '7' and resid 224 through 227 Processing helix chain '7' and resid 319 through 328 removed outlier: 4.196A pdb=" N GLU 7 325 " --> pdb=" O PRO 7 321 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLU 7 326 " --> pdb=" O GLU 7 322 " (cutoff:3.500A) Processing helix chain '7' and resid 333 through 339 removed outlier: 3.733A pdb=" N ALA 7 337 " --> pdb=" O TYR 7 333 " (cutoff:3.500A) Processing helix chain '7' and resid 349 through 360 removed outlier: 4.588A pdb=" N ALA 7 353 " --> pdb=" O ASP 7 349 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU 7 357 " --> pdb=" O ALA 7 353 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 7 358 " --> pdb=" O LEU 7 354 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL 7 359 " --> pdb=" O LEU 7 355 " (cutoff:3.500A) Processing helix chain '7' and resid 365 through 369 removed outlier: 3.713A pdb=" N GLY 7 368 " --> pdb=" O ARG 7 365 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 398 removed outlier: 3.578A pdb=" N ARG 7 396 " --> pdb=" O GLY 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 414 removed outlier: 3.895A pdb=" N LEU 7 414 " --> pdb=" O GLY 7 411 " (cutoff:3.500A) Processing helix chain '7' and resid 432 through 437 Processing helix chain '7' and resid 453 through 460 removed outlier: 3.504A pdb=" N GLU 7 460 " --> pdb=" O THR 7 456 " (cutoff:3.500A) Processing helix chain '7' and resid 461 through 463 No H-bonds generated for 'chain '7' and resid 461 through 463' Processing helix chain '7' and resid 508 through 514 Processing helix chain '7' and resid 528 through 543 removed outlier: 3.896A pdb=" N LYS 7 535 " --> pdb=" O LEU 7 531 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS 7 536 " --> pdb=" O ARG 7 532 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR 7 539 " --> pdb=" O LYS 7 535 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER 7 542 " --> pdb=" O THR 7 538 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS 7 543 " --> pdb=" O TYR 7 539 " (cutoff:3.500A) Processing helix chain '7' and resid 555 through 568 removed outlier: 3.635A pdb=" N LEU 7 565 " --> pdb=" O ARG 7 561 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG 7 568 " --> pdb=" O ASN 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 576 No H-bonds generated for 'chain '7' and resid 574 through 576' Processing helix chain '7' and resid 577 through 591 removed outlier: 4.375A pdb=" N VAL 7 582 " --> pdb=" O THR 7 578 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY 7 583 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) Processing helix chain '7' and resid 604 through 621 removed outlier: 3.905A pdb=" N LEU 7 610 " --> pdb=" O LEU 7 606 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG 7 611 " --> pdb=" O LEU 7 607 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR 7 614 " --> pdb=" O LEU 7 610 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA 7 617 " --> pdb=" O SER 7 613 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG 7 618 " --> pdb=" O THR 7 614 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU 7 619 " --> pdb=" O ALA 7 615 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 641 removed outlier: 3.632A pdb=" N VAL 7 630 " --> pdb=" O GLU 7 626 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG 7 635 " --> pdb=" O ALA 7 631 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS 7 641 " --> pdb=" O LEU 7 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 14 Processing helix chain 'A' and resid 26 through 41 removed outlier: 3.550A pdb=" N ILE A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE A 35 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 126 through 130 removed outlier: 4.325A pdb=" N PHE A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 201 removed outlier: 3.696A pdb=" N GLN A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 229 through 243 removed outlier: 4.533A pdb=" N GLN A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 4.715A pdb=" N GLU A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.923A pdb=" N SER A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.688A pdb=" N GLN A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 4.082A pdb=" N GLU A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.513A pdb=" N GLN A 340 " --> pdb=" O HIS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 removed outlier: 4.038A pdb=" N ARG A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'A' and resid 422 through 449 removed outlier: 3.848A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 440 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 490 removed outlier: 3.963A pdb=" N LEU A 476 " --> pdb=" O TYR A 472 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ARG A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.812A pdb=" N ALA A 539 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 570 Processing helix chain 'H' and resid 11 through 16 Processing helix chain 'H' and resid 17 through 20 Processing helix chain 'H' and resid 40 through 49 removed outlier: 3.851A pdb=" N PHE H 45 " --> pdb=" O ILE H 41 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLU H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 62 No H-bonds generated for 'chain 'H' and resid 60 through 62' Processing helix chain 'H' and resid 63 through 96 removed outlier: 3.951A pdb=" N ASN H 68 " --> pdb=" O TRP H 64 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG H 88 " --> pdb=" O TYR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 Processing helix chain 'L' and resid 6 through 11 Processing helix chain 'L' and resid 48 through 54 removed outlier: 3.613A pdb=" N LYS L 54 " --> pdb=" O THR L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 81 removed outlier: 5.156A pdb=" N LYS L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 101 removed outlier: 3.980A pdb=" N GLN L 97 " --> pdb=" O MET L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 106 Processing helix chain 'L' and resid 111 through 131 removed outlier: 3.892A pdb=" N ILE L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 135 Processing helix chain 'L' and resid 149 through 154 removed outlier: 4.170A pdb=" N ILE L 153 " --> pdb=" O THR L 149 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS L 154 " --> pdb=" O LEU L 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 149 through 154' Processing helix chain 'L' and resid 158 through 168 removed outlier: 4.192A pdb=" N TYR L 162 " --> pdb=" O PRO L 158 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER L 163 " --> pdb=" O ILE L 159 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N HIS L 166 " --> pdb=" O TYR L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 173 Processing helix chain 'L' and resid 174 through 177 removed outlier: 3.718A pdb=" N SER L 177 " --> pdb=" O ALA L 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 174 through 177' Processing helix chain 'M' and resid 57 through 62 removed outlier: 3.849A pdb=" N GLU M 61 " --> pdb=" O TYR M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 88 removed outlier: 4.090A pdb=" N LYS M 82 " --> pdb=" O ARG M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 109 Processing helix chain 'M' and resid 110 through 112 No H-bonds generated for 'chain 'M' and resid 110 through 112' Processing helix chain 'M' and resid 116 through 132 removed outlier: 3.889A pdb=" N ARG M 128 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU M 132 " --> pdb=" O ARG M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 171 removed outlier: 3.858A pdb=" N LEU M 156 " --> pdb=" O ILE M 152 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU M 169 " --> pdb=" O SER M 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 51 removed outlier: 4.435A pdb=" N ILE N 42 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR N 44 " --> pdb=" O GLU N 40 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA N 45 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET N 50 " --> pdb=" O TRP N 46 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS N 51 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 80 removed outlier: 4.043A pdb=" N VAL N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU N 80 " --> pdb=" O GLN N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 115 Processing helix chain 'N' and resid 118 through 127 removed outlier: 3.627A pdb=" N GLN N 122 " --> pdb=" O HIS N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 153 Processing helix chain 'N' and resid 218 through 223 Processing sheet with id=AA1, first strand: chain '2' and resid 216 through 217 Processing sheet with id=AA2, first strand: chain '2' and resid 296 through 298 removed outlier: 4.474A pdb=" N THR 2 362 " --> pdb=" O THR 2 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 296 through 298 removed outlier: 4.474A pdb=" N THR 2 362 " --> pdb=" O THR 2 298 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN 2 359 " --> pdb=" O LEU 2 383 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS 2 379 " --> pdb=" O LEU 2 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 310 through 312 removed outlier: 4.077A pdb=" N ILE 2 310 " --> pdb=" O PHE 2 324 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR 2 312 " --> pdb=" O GLY 2 322 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY 2 322 " --> pdb=" O TYR 2 312 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 397 through 399 Processing sheet with id=AA6, first strand: chain '2' and resid 505 through 506 removed outlier: 6.503A pdb=" N LEU 2 505 " --> pdb=" O CYS 2 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '3' and resid 135 through 136 removed outlier: 4.069A pdb=" N ARG 3 135 " --> pdb=" O HIS 3 193 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN 3 194 " --> pdb=" O CYS 3 218 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU 3 196 " --> pdb=" O ILE 3 216 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA 3 259 " --> pdb=" O VAL 3 217 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN 3 260 " --> pdb=" O VAL 3 235 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL 3 235 " --> pdb=" O ASN 3 260 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE 3 262 " --> pdb=" O GLN 3 233 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN 3 233 " --> pdb=" O ILE 3 262 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU 3 264 " --> pdb=" O ARG 3 231 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ARG 3 231 " --> pdb=" O LEU 3 264 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN 3 199 " --> pdb=" O ILE 3 127 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR 3 129 " --> pdb=" O THR 3 197 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR 3 197 " --> pdb=" O THR 3 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 140 through 142 Processing sheet with id=AA9, first strand: chain '3' and resid 322 through 323 removed outlier: 4.717A pdb=" N LYS 3 322 " --> pdb=" O LEU 3 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '4' and resid 317 through 319 removed outlier: 4.065A pdb=" N VAL 4 318 " --> pdb=" O ALA 4 305 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA 4 305 " --> pdb=" O VAL 4 318 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG 4 341 " --> pdb=" O SER 4 308 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '4' and resid 355 through 357 Processing sheet with id=AB3, first strand: chain '4' and resid 391 through 394 removed outlier: 3.563A pdb=" N THR 4 392 " --> pdb=" O ARG 4 425 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS 4 423 " --> pdb=" O THR 4 394 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '4' and resid 397 through 400 Processing sheet with id=AB5, first strand: chain '4' and resid 411 through 412 Processing sheet with id=AB6, first strand: chain '4' and resid 532 through 534 removed outlier: 6.396A pdb=" N GLN 4 533 " --> pdb=" O CYS 4 574 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '4' and resid 550 through 552 removed outlier: 4.174A pdb=" N THR 4 550 " --> pdb=" O VAL 4 559 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL 4 559 " --> pdb=" O THR 4 550 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 600 through 601 Processing sheet with id=AB9, first strand: chain '5' and resid 64 through 65 removed outlier: 3.737A pdb=" N LEU 5 65 " --> pdb=" O GLN 5 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain '5' and resid 164 through 165 removed outlier: 4.295A pdb=" N SER 5 164 " --> pdb=" O MET 5 210 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '5' and resid 223 through 225 Processing sheet with id=AC3, first strand: chain '5' and resid 262 through 264 Processing sheet with id=AC4, first strand: chain '5' and resid 481 through 485 removed outlier: 4.208A pdb=" N GLY 5 378 " --> pdb=" O ALA 5 485 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET 5 513 " --> pdb=" O ASN 5 373 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '5' and resid 572 through 573 removed outlier: 7.588A pdb=" N ARG 5 572 " --> pdb=" O ALA 5 631 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain '6' and resid 198 through 202 removed outlier: 3.846A pdb=" N GLN 6 198 " --> pdb=" O LEU 6 222 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU 6 222 " --> pdb=" O GLN 6 198 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '6' and resid 241 through 242 removed outlier: 3.767A pdb=" N THR 6 241 " --> pdb=" O LEU 6 291 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU 6 291 " --> pdb=" O THR 6 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '6' and resid 387 through 388 removed outlier: 6.656A pdb=" N VAL 6 387 " --> pdb=" O LEU 6 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '7' and resid 162 through 168 removed outlier: 9.378A pdb=" N LEU 7 298 " --> pdb=" O SER 7 252 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR 7 254 " --> pdb=" O LEU 7 298 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ALA 7 300 " --> pdb=" O THR 7 254 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET 7 256 " --> pdb=" O ALA 7 300 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ARG 7 302 " --> pdb=" O MET 7 256 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER 7 274 " --> pdb=" O HIS 7 301 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE 7 303 " --> pdb=" O VAL 7 272 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL 7 272 " --> pdb=" O ILE 7 303 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '7' and resid 175 through 177 Processing sheet with id=AD2, first strand: chain '7' and resid 193 through 194 removed outlier: 3.593A pdb=" N ALA 7 180 " --> pdb=" O GLN 7 193 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR 7 181 " --> pdb=" O GLN 7 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '7' and resid 376 through 377 removed outlier: 3.660A pdb=" N CYS 7 442 " --> pdb=" O SER 7 483 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU 7 485 " --> pdb=" O CYS 7 442 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLN 7 402 " --> pdb=" O CYS 7 443 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '7' and resid 417 through 418 Processing sheet with id=AD5, first strand: chain 'A' and resid 49 through 50 removed outlier: 9.693A pdb=" N VAL A 50 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU A 20 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 501 through 505 removed outlier: 3.707A pdb=" N ALA A 503 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 516 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 556 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 14 through 17 Processing sheet with id=AD8, first strand: chain 'N' and resid 183 through 184 1092 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13140 1.34 - 1.46: 9190 1.46 - 1.59: 18943 1.59 - 1.71: 83 1.71 - 1.84: 377 Bond restraints: 41733 Sorted by residual: bond pdb=" C4 ATP 3 901 " pdb=" C5 ATP 3 901 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.71e+01 bond pdb=" C4 ATP 5 801 " pdb=" C5 ATP 5 801 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.60e+01 bond pdb=" C4 ATP 2 901 " pdb=" C5 ATP 2 901 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.08e+01 bond pdb=" C5 ATP 5 801 " pdb=" C6 ATP 5 801 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.11e+01 bond pdb=" C5 ATP 2 901 " pdb=" C6 ATP 2 901 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.42e+01 ... (remaining 41728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.50: 55992 5.50 - 10.99: 460 10.99 - 16.49: 38 16.49 - 21.98: 9 21.98 - 27.48: 3 Bond angle restraints: 56502 Sorted by residual: angle pdb=" PB ATP 3 901 " pdb=" O3B ATP 3 901 " pdb=" PG ATP 3 901 " ideal model delta sigma weight residual 139.87 117.79 22.08 1.00e+00 1.00e+00 4.87e+02 angle pdb=" PB ATP 5 801 " pdb=" O3B ATP 5 801 " pdb=" PG ATP 5 801 " ideal model delta sigma weight residual 139.87 118.58 21.29 1.00e+00 1.00e+00 4.53e+02 angle pdb=" PA ATP 2 901 " pdb=" O3A ATP 2 901 " pdb=" PB ATP 2 901 " ideal model delta sigma weight residual 136.83 117.36 19.47 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP 5 801 " pdb=" O3A ATP 5 801 " pdb=" PB ATP 5 801 " ideal model delta sigma weight residual 136.83 117.38 19.45 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PA ATP 3 901 " pdb=" O3A ATP 3 901 " pdb=" PB ATP 3 901 " ideal model delta sigma weight residual 136.83 118.33 18.50 1.00e+00 1.00e+00 3.42e+02 ... (remaining 56497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 24561 34.93 - 69.86: 883 69.86 - 104.79: 71 104.79 - 139.72: 3 139.72 - 174.65: 1 Dihedral angle restraints: 25519 sinusoidal: 10714 harmonic: 14805 Sorted by residual: dihedral pdb=" CA ASP 7 382 " pdb=" C ASP 7 382 " pdb=" N PRO 7 383 " pdb=" CA PRO 7 383 " ideal model delta harmonic sigma weight residual -180.00 -119.40 -60.60 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA THR A 490 " pdb=" C THR A 490 " pdb=" N SER A 491 " pdb=" CA SER A 491 " ideal model delta harmonic sigma weight residual 180.00 133.21 46.79 0 5.00e+00 4.00e-02 8.76e+01 dihedral pdb=" CA ILE 4 615 " pdb=" C ILE 4 615 " pdb=" N LEU 4 616 " pdb=" CA LEU 4 616 " ideal model delta harmonic sigma weight residual 180.00 136.47 43.53 0 5.00e+00 4.00e-02 7.58e+01 ... (remaining 25516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.584: 6338 0.584 - 1.169: 3 1.169 - 1.753: 17 1.753 - 2.338: 3 2.338 - 2.922: 1 Chirality restraints: 6362 Sorted by residual: chirality pdb=" CB VAL 5 432 " pdb=" CA VAL 5 432 " pdb=" CG1 VAL 5 432 " pdb=" CG2 VAL 5 432 " both_signs ideal model delta sigma weight residual False -2.63 0.29 -2.92 2.00e-01 2.50e+01 2.14e+02 chirality pdb=" CB ILE 2 585 " pdb=" CA ILE 2 585 " pdb=" CG1 ILE 2 585 " pdb=" CG2 ILE 2 585 " both_signs ideal model delta sigma weight residual False 2.64 0.66 1.99 2.00e-01 2.50e+01 9.89e+01 chirality pdb=" CB VAL 2 463 " pdb=" CA VAL 2 463 " pdb=" CG1 VAL 2 463 " pdb=" CG2 VAL 2 463 " both_signs ideal model delta sigma weight residual False -2.63 -0.68 -1.95 2.00e-01 2.50e+01 9.50e+01 ... (remaining 6359 not shown) Planarity restraints: 7230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 521 " -0.425 9.50e-02 1.11e+02 2.21e-01 1.78e+02 pdb=" NE ARG 6 521 " 0.105 2.00e-02 2.50e+03 pdb=" CZ ARG 6 521 " -0.210 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 521 " 0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 521 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG 5 199 " -0.100 5.00e-02 4.00e+02 1.53e-01 3.74e+01 pdb=" N PRO 5 200 " 0.264 5.00e-02 4.00e+02 pdb=" CA PRO 5 200 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO 5 200 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 4 513 " -0.082 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO 4 514 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO 4 514 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO 4 514 " -0.066 5.00e-02 4.00e+02 ... (remaining 7227 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 8 2.03 - 2.74: 6121 2.74 - 3.46: 64089 3.46 - 4.18: 98377 4.18 - 4.90: 160140 Nonbonded interactions: 328735 Sorted by model distance: nonbonded pdb=" OG SER 3 347 " pdb=" O1B ATP 3 901 " model vdw 1.308 3.040 nonbonded pdb=" CB SER 3 347 " pdb=" O1B ATP 3 901 " model vdw 1.373 3.440 nonbonded pdb=" O ILE A 237 " pdb=" OG1 THR A 241 " model vdw 1.971 3.040 nonbonded pdb=" O GLU 2 278 " pdb=" OG1 THR 2 281 " model vdw 1.998 3.040 nonbonded pdb=" O GLU L 90 " pdb=" OG1 THR L 149 " model vdw 2.002 3.040 ... (remaining 328730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 35.680 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5768 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.891 41741 Z= 0.675 Angle : 1.464 27.476 56508 Z= 0.813 Chirality : 0.127 2.922 6362 Planarity : 0.009 0.221 7230 Dihedral : 18.035 174.646 15900 Min Nonbonded Distance : 1.308 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.48 % Allowed : 19.24 % Favored : 80.28 % Rotamer: Outliers : 6.70 % Allowed : 15.27 % Favored : 78.03 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.05 % Twisted General : 0.95 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.61 (0.09), residues: 5000 helix: -3.27 (0.09), residues: 1545 sheet: -4.59 (0.15), residues: 465 loop : -4.03 (0.10), residues: 2990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.215 0.003 ARG 6 521 TYR 0.063 0.004 TYR N 104 PHE 0.041 0.005 PHE M 17 TRP 0.029 0.005 TRP M 170 HIS 0.020 0.004 HIS M 115 Details of bonding type rmsd/Z covalent geometry : bond 0.01137 / 0.52 (41733) covalent geometry : angle 1.46095 / 0.81 (56502) SS BOND : bond 0.01666 / 0.87 ( 3) SS BOND : angle 9.79356 / 5.39 ( 6) hydrogen bonds : bond 0.21269 / 14.43 ( 1089) hydrogen bonds : angle 8.98989 / 6.08 ( 3105) Misc. bond : bond 0.39829 / 19.92 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 297 poor density : 961 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 212 MET cc_start: 0.7591 (mmp) cc_final: 0.5611 (ttp) REVERT: 2 271 SER cc_start: 0.5576 (OUTLIER) cc_final: 0.5199 (t) REVERT: 2 284 LYS cc_start: 0.6311 (pptt) cc_final: 0.5987 (tttm) REVERT: 2 553 GLU cc_start: 0.6522 (mp0) cc_final: 0.5204 (tp30) REVERT: 2 568 VAL cc_start: 0.4054 (OUTLIER) cc_final: 0.3693 (p) REVERT: 2 626 MET cc_start: -0.0253 (ttt) cc_final: -0.0505 (mtt) REVERT: 2 666 HIS cc_start: 0.8439 (t70) cc_final: 0.8231 (t70) REVERT: 2 722 LYS cc_start: 0.6548 (mptt) cc_final: 0.6281 (ptmm) REVERT: 2 752 GLU cc_start: 0.6432 (pt0) cc_final: 0.5848 (pt0) REVERT: 3 85 ASP cc_start: 0.8161 (t0) cc_final: 0.7773 (t0) REVERT: 3 221 ASP cc_start: 0.6922 (m-30) cc_final: 0.6636 (t0) REVERT: 3 226 CYS cc_start: 0.3352 (t) cc_final: 0.3121 (t) REVERT: 3 265 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7023 (pp) REVERT: 3 296 LYS cc_start: 0.6419 (mttt) cc_final: 0.5854 (pttt) REVERT: 3 348 GLN cc_start: 0.5223 (OUTLIER) cc_final: 0.4224 (tp40) REVERT: 3 458 LYS cc_start: 0.6945 (tmmt) cc_final: 0.5784 (mmmt) REVERT: 3 470 LEU cc_start: 0.5901 (mp) cc_final: 0.5260 (pp) REVERT: 3 525 PHE cc_start: 0.5387 (m-10) cc_final: 0.5039 (m-80) REVERT: 3 572 MET cc_start: 0.7074 (mmp) cc_final: 0.6654 (mmp) REVERT: 3 641 GLU cc_start: 0.5762 (mt-10) cc_final: 0.5012 (tp30) REVERT: 4 188 ASN cc_start: 0.6025 (m-40) cc_final: 0.5664 (p0) REVERT: 4 193 GLN cc_start: 0.5552 (tt0) cc_final: 0.5059 (tm-30) REVERT: 4 278 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7401 (m-40) REVERT: 4 424 PHE cc_start: 0.6929 (m-80) cc_final: 0.6704 (m-80) REVERT: 4 558 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5593 (mm) REVERT: 4 590 HIS cc_start: 0.5073 (OUTLIER) cc_final: 0.4063 (m170) REVERT: 4 595 GLN cc_start: 0.8242 (mt0) cc_final: 0.7129 (mm-40) REVERT: 4 645 ARG cc_start: 0.2379 (OUTLIER) cc_final: 0.2095 (tmt-80) REVERT: 4 647 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6502 (m-30) REVERT: 4 653 LEU cc_start: 0.4993 (pt) cc_final: 0.4384 (tp) REVERT: 4 676 ARG cc_start: 0.3033 (pmt-80) cc_final: 0.1451 (ppt170) REVERT: 4 680 GLU cc_start: 0.1557 (pm20) cc_final: 0.0396 (mt-10) REVERT: 5 68 GLU cc_start: 0.5551 (pt0) cc_final: 0.5121 (pt0) REVERT: 5 71 ASP cc_start: 0.7275 (p0) cc_final: 0.6869 (p0) REVERT: 5 216 CYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6295 (p) REVERT: 5 239 HIS cc_start: 0.7775 (p90) cc_final: 0.7570 (p-80) REVERT: 5 241 GLN cc_start: 0.4793 (pt0) cc_final: 0.4507 (mm-40) REVERT: 5 257 ARG cc_start: 0.6559 (mtm180) cc_final: 0.6068 (ptp-110) REVERT: 5 307 ARG cc_start: 0.5655 (OUTLIER) cc_final: 0.5137 (pmt170) REVERT: 5 360 LYS cc_start: 0.3016 (mmtt) cc_final: 0.2658 (mmtp) REVERT: 5 379 ASP cc_start: 0.7075 (t0) cc_final: 0.6691 (t0) REVERT: 5 402 SER cc_start: 0.6943 (OUTLIER) cc_final: 0.6697 (t) REVERT: 5 417 LYS cc_start: 0.7944 (pttt) cc_final: 0.7052 (pttt) REVERT: 5 443 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: 5 514 ILE cc_start: 0.4010 (mp) cc_final: 0.3768 (mp) REVERT: 5 588 MET cc_start: 0.6800 (tpp) cc_final: 0.5673 (tpp) REVERT: 5 641 ARG cc_start: 0.6202 (mmt180) cc_final: 0.5980 (mmm160) REVERT: 6 16 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6158 (tp30) REVERT: 6 55 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.5032 (pt) REVERT: 6 90 ASN cc_start: 0.7782 (m110) cc_final: 0.7527 (m-40) REVERT: 6 116 LYS cc_start: 0.5981 (mmtt) cc_final: 0.5597 (ttmm) REVERT: 6 220 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6477 (mm) REVERT: 6 284 LEU cc_start: 0.2619 (OUTLIER) cc_final: 0.2228 (pp) REVERT: 6 296 GLN cc_start: 0.7603 (tp-100) cc_final: 0.6713 (tt0) REVERT: 6 309 MET cc_start: 0.2657 (mtp) cc_final: 0.1375 (tmm) REVERT: 6 325 GLU cc_start: 0.6290 (mp0) cc_final: 0.5211 (mp0) REVERT: 6 332 MET cc_start: 0.4115 (mpp) cc_final: 0.2237 (tpt) REVERT: 6 410 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.3111 (t80) REVERT: 6 537 ASP cc_start: 0.7255 (m-30) cc_final: 0.6939 (m-30) REVERT: 6 612 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7134 (mt0) REVERT: 6 639 GLU cc_start: 0.4315 (tt0) cc_final: 0.4033 (mt-10) REVERT: 7 57 GLU cc_start: 0.6852 (tt0) cc_final: 0.6315 (mp0) REVERT: 7 83 GLU cc_start: 0.5046 (mm-30) cc_final: 0.3981 (tp30) REVERT: 7 131 MET cc_start: 0.6273 (ptm) cc_final: 0.5901 (tmm) REVERT: 7 223 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8443 (tp-100) REVERT: 7 281 MET cc_start: 0.7784 (mtm) cc_final: 0.7117 (mtp) REVERT: 7 282 ARG cc_start: 0.6986 (tmt-80) cc_final: 0.5897 (ttm-80) REVERT: 7 419 MET cc_start: -0.4666 (ttp) cc_final: -0.5333 (mmt) REVERT: 7 494 ARG cc_start: 0.3790 (ptm-80) cc_final: 0.2557 (ttm170) REVERT: 7 527 ARG cc_start: 0.7229 (ttp80) cc_final: 0.6026 (mmt180) REVERT: 7 536 HIS cc_start: 0.5355 (m90) cc_final: 0.5081 (m-70) REVERT: 7 556 MET cc_start: 0.2602 (ptm) cc_final: 0.1666 (tmm) REVERT: 7 589 ARG cc_start: 0.7278 (mtp180) cc_final: 0.6991 (mtp85) REVERT: 7 634 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5875 (mt) REVERT: 7 635 ARG cc_start: 0.6370 (ptm-80) cc_final: 0.6074 (tpp-160) REVERT: A 53 MET cc_start: 0.4975 (mpp) cc_final: 0.4126 (ttp) REVERT: A 65 HIS cc_start: 0.8701 (m90) cc_final: 0.8426 (m170) REVERT: A 223 TRP cc_start: 0.6285 (t60) cc_final: 0.5816 (t60) REVERT: A 460 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7645 (t80) REVERT: A 567 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5597 (tt) REVERT: H 16 LEU cc_start: 0.2950 (OUTLIER) cc_final: 0.2668 (mp) REVERT: H 70 ARG cc_start: 0.7774 (tmm160) cc_final: 0.7324 (tmm160) REVERT: H 88 ARG cc_start: 0.6762 (mmt180) cc_final: 0.5624 (mmt180) REVERT: L 119 ASP cc_start: 0.7719 (t70) cc_final: 0.7510 (t0) REVERT: N 60 THR cc_start: 0.7518 (p) cc_final: 0.7059 (m) REVERT: N 107 CYS cc_start: 0.5726 (OUTLIER) cc_final: 0.4463 (m) REVERT: N 151 TYR cc_start: 0.4065 (t80) cc_final: 0.3626 (t80) outliers start: 297 outliers final: 120 residues processed: 1214 average time/residue: 0.2645 time to fit residues: 515.4148 Evaluate side-chains 785 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 642 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 307 LEU Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 381 VAL Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 442 THR Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 518 LEU Chi-restraints excluded: chain 2 residue 531 THR Chi-restraints excluded: chain 2 residue 532 THR Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 565 ASP Chi-restraints excluded: chain 2 residue 568 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 605 LEU Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 727 LEU Chi-restraints excluded: chain 2 residue 743 HIS Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 256 VAL Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 301 SER Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 341 ASP Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 374 THR Chi-restraints excluded: chain 3 residue 400 VAL Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 4 residue 237 ILE Chi-restraints excluded: chain 4 residue 276 SER Chi-restraints excluded: chain 4 residue 278 ASN Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 510 LEU Chi-restraints excluded: chain 4 residue 516 THR Chi-restraints excluded: chain 4 residue 549 VAL Chi-restraints excluded: chain 4 residue 558 LEU Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 605 ILE Chi-restraints excluded: chain 4 residue 638 LEU Chi-restraints excluded: chain 4 residue 645 ARG Chi-restraints excluded: chain 4 residue 647 ASP Chi-restraints excluded: chain 4 residue 740 ILE Chi-restraints excluded: chain 5 residue 38 ILE Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 137 SER Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 253 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 313 SER Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 387 LEU Chi-restraints excluded: chain 5 residue 402 SER Chi-restraints excluded: chain 5 residue 441 ILE Chi-restraints excluded: chain 5 residue 443 GLU Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 464 ILE Chi-restraints excluded: chain 5 residue 502 ASP Chi-restraints excluded: chain 5 residue 536 VAL Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 567 THR Chi-restraints excluded: chain 5 residue 636 VAL Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 398 LEU Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 451 ILE Chi-restraints excluded: chain 6 residue 546 ASP Chi-restraints excluded: chain 6 residue 609 THR Chi-restraints excluded: chain 6 residue 612 GLN Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 269 ASP Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 356 LEU Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 634 LEU Chi-restraints excluded: chain 7 residue 644 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 CYS Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 110 CYS Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 151 ASN Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 0.0030 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 494 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 267 HIS 2 306 GLN 2 352 GLN 2 390 GLN 2 412 ASN 2 534 GLN 2 548 ASN 2 592 GLN 2 631 ASN 2 659 GLN ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 694 GLN 2 762 ASN ** 2 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 13 GLN 3 57 GLN 3 348 GLN 3 434 HIS 3 448 ASN 3 504 ASN 4 182 GLN 4 214 ASN 4 223 GLN 4 260 GLN 4 267 ASN 4 326 ASN 4 344 HIS 4 378 HIS ** 4 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 627 ASN 4 699 HIS 4 735 GLN ** 4 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 21 GLN 5 120 GLN ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 256 ASN 5 334 GLN 5 373 ASN ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 462 GLN 5 486 ASN 5 532 HIS ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 644 GLN 6 134 GLN 6 198 GLN 6 383 ASN 6 533 ASN 6 612 GLN 7 42 HIS ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 214 ASN 7 347 HIS ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 439 GLN ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 645 ASN A 312 GLN A 421 HIS A 436 HIS A 464 GLN A 467 HIS ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN H 68 ASN H 109 GLN H 120 ASN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN L 91 HIS L 147 ASN ** L 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 HIS M 164 ASN N 59 GLN N 153 HIS N 164 GLN N 208 GLN N 214 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.272794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5066 r_free = 0.5066 target = 0.260763 restraints weight = 73997.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.260912 restraints weight = 86030.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.259906 restraints weight = 57580.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.259854 restraints weight = 54549.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.260039 restraints weight = 50200.307| |-----------------------------------------------------------------------------| r_work (final): 0.5061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5327 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 41741 Z= 0.203 Angle : 0.953 12.825 56508 Z= 0.490 Chirality : 0.052 0.357 6362 Planarity : 0.007 0.083 7230 Dihedral : 13.231 138.321 6127 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.80 % Favored : 86.18 % Rotamer: Outliers : 5.91 % Allowed : 19.31 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.10), residues: 5000 helix: -2.37 (0.11), residues: 1593 sheet: -3.78 (0.18), residues: 507 loop : -3.70 (0.10), residues: 2900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 129 TYR 0.037 0.002 TYR 3 16 PHE 0.029 0.003 PHE 7 134 TRP 0.028 0.003 TRP M 170 HIS 0.018 0.002 HIS 5 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (41733) covalent geometry : angle 0.95324 / 0.49 (56502) SS BOND : bond 0.00217 / 0.11 ( 3) SS BOND : angle 1.49126 / 0.61 ( 6) hydrogen bonds : bond 0.06249 / 4.14 ( 1089) hydrogen bonds : angle 7.19679 / 4.88 ( 3105) Misc. bond : bond 0.01726 / 0.86 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 769 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 212 MET cc_start: 0.6983 (mmp) cc_final: 0.6169 (ttp) REVERT: 2 271 SER cc_start: 0.5568 (OUTLIER) cc_final: 0.5110 (t) REVERT: 2 389 ASP cc_start: 0.5973 (t70) cc_final: 0.5553 (t0) REVERT: 2 397 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.7022 (mt) REVERT: 2 488 GLU cc_start: 0.4743 (mm-30) cc_final: 0.3990 (mm-30) REVERT: 2 752 GLU cc_start: 0.5234 (pt0) cc_final: 0.4675 (pt0) REVERT: 3 39 GLU cc_start: 0.8090 (mp0) cc_final: 0.7827 (mp0) REVERT: 3 190 TYR cc_start: 0.5141 (p90) cc_final: 0.4668 (p90) REVERT: 3 221 ASP cc_start: 0.6184 (m-30) cc_final: 0.5563 (t0) REVERT: 3 253 PHE cc_start: 0.5729 (OUTLIER) cc_final: 0.5338 (t80) REVERT: 3 348 GLN cc_start: 0.5511 (OUTLIER) cc_final: 0.5115 (tp40) REVERT: 3 458 LYS cc_start: 0.6115 (tmmt) cc_final: 0.5387 (mmmt) REVERT: 3 462 GLU cc_start: 0.6710 (tp30) cc_final: 0.6175 (tp30) REVERT: 3 470 LEU cc_start: 0.5941 (mp) cc_final: 0.5646 (pp) REVERT: 4 513 ASP cc_start: 0.6577 (m-30) cc_final: 0.6242 (p0) REVERT: 4 524 TYR cc_start: 0.5480 (OUTLIER) cc_final: 0.5138 (m-80) REVERT: 4 590 HIS cc_start: 0.5779 (OUTLIER) cc_final: 0.5467 (m170) REVERT: 4 593 MET cc_start: 0.3722 (mtm) cc_final: 0.3393 (tmm) REVERT: 4 680 GLU cc_start: 0.1788 (pm20) cc_final: 0.0768 (mt-10) REVERT: 5 42 ASN cc_start: 0.6488 (m-40) cc_final: 0.5727 (t0) REVERT: 5 216 CYS cc_start: 0.5718 (OUTLIER) cc_final: 0.5284 (p) REVERT: 5 360 LYS cc_start: 0.3485 (mmtt) cc_final: 0.2804 (mmtp) REVERT: 5 379 ASP cc_start: 0.7585 (t0) cc_final: 0.7289 (t0) REVERT: 6 80 ILE cc_start: 0.6230 (mt) cc_final: 0.4971 (mt) REVERT: 6 151 MET cc_start: 0.2834 (tmm) cc_final: 0.2476 (ttp) REVERT: 6 219 GLU cc_start: 0.5701 (mp0) cc_final: 0.5356 (mp0) REVERT: 6 284 LEU cc_start: 0.3617 (OUTLIER) cc_final: 0.2869 (pp) REVERT: 6 309 MET cc_start: 0.2524 (mtp) cc_final: 0.0469 (tmm) REVERT: 6 332 MET cc_start: 0.3282 (mpp) cc_final: 0.2966 (tpt) REVERT: 6 410 TYR cc_start: 0.4923 (OUTLIER) cc_final: 0.3494 (t80) REVERT: 6 586 LEU cc_start: 0.3772 (OUTLIER) cc_final: 0.3565 (tt) REVERT: 6 612 GLN cc_start: 0.7606 (mp10) cc_final: 0.6640 (mt0) REVERT: 7 80 VAL cc_start: 0.6816 (OUTLIER) cc_final: 0.6605 (t) REVERT: 7 83 GLU cc_start: 0.5087 (mm-30) cc_final: 0.4875 (pp20) REVERT: 7 281 MET cc_start: 0.6416 (mtm) cc_final: 0.6195 (mtp) REVERT: 7 282 ARG cc_start: 0.7528 (tmt-80) cc_final: 0.6958 (ttm-80) REVERT: 7 294 SER cc_start: 0.6899 (OUTLIER) cc_final: 0.6518 (p) REVERT: 7 419 MET cc_start: -0.1101 (ttp) cc_final: -0.4008 (mmt) REVERT: 7 494 ARG cc_start: 0.3977 (ptm-80) cc_final: 0.2593 (ttm170) REVERT: 7 511 LEU cc_start: 0.3787 (OUTLIER) cc_final: 0.3549 (mt) REVERT: A 53 MET cc_start: 0.4088 (mpp) cc_final: 0.3544 (ttp) REVERT: A 65 HIS cc_start: 0.7247 (m90) cc_final: 0.6913 (m170) REVERT: A 304 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6069 (tmm-80) REVERT: L 120 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7068 (mm) REVERT: M 113 ARG cc_start: 0.3658 (mmp-170) cc_final: 0.2832 (tpt-90) REVERT: N 82 LYS cc_start: 0.5750 (mppt) cc_final: 0.5154 (pttm) outliers start: 262 outliers final: 117 residues processed: 968 average time/residue: 0.2657 time to fit residues: 414.5199 Evaluate side-chains 734 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 602 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 397 LEU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 531 THR Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 569 CYS Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 605 LEU Chi-restraints excluded: chain 2 residue 611 VAL Chi-restraints excluded: chain 2 residue 640 SER Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 374 THR Chi-restraints excluded: chain 3 residue 400 VAL Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 528 SER Chi-restraints excluded: chain 3 residue 624 ARG Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 478 ILE Chi-restraints excluded: chain 4 residue 510 LEU Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 592 VAL Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 685 ASP Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 313 SER Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 636 VAL Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 281 MET Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 546 ASP Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 6 residue 586 LEU Chi-restraints excluded: chain 6 residue 609 THR Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 294 SER Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 350 VAL Chi-restraints excluded: chain 7 residue 421 ASP Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 514 CYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 164 ASN Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 130 optimal weight: 0.4980 chunk 191 optimal weight: 0.9980 chunk 340 optimal weight: 0.0570 chunk 109 optimal weight: 0.6980 chunk 418 optimal weight: 0.7980 chunk 233 optimal weight: 0.9980 chunk 467 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 310 optimal weight: 6.9990 chunk 444 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 659 GLN ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 699 GLN 3 143 HIS 3 233 GLN ** 4 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 523 GLN ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 334 GLN ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 HIS ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 79 HIS 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 193 GLN ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS A 154 HIS ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN H 109 GLN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 147 ASN L 166 HIS N 117 GLN N 153 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5172 r_free = 0.5172 target = 0.273748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.261114 restraints weight = 73941.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.260821 restraints weight = 85210.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.261317 restraints weight = 68806.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.260847 restraints weight = 56517.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.261245 restraints weight = 53848.259| |-----------------------------------------------------------------------------| r_work (final): 0.5069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5322 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 41741 Z= 0.170 Angle : 0.839 13.784 56508 Z= 0.431 Chirality : 0.049 0.236 6362 Planarity : 0.006 0.075 7230 Dihedral : 12.175 136.732 5987 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.82 % Favored : 86.16 % Rotamer: Outliers : 5.41 % Allowed : 21.25 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.05 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.10), residues: 5000 helix: -1.86 (0.12), residues: 1637 sheet: -3.41 (0.19), residues: 501 loop : -3.51 (0.10), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 3 473 TYR 0.030 0.002 TYR 6 236 PHE 0.031 0.002 PHE 7 77 TRP 0.041 0.002 TRP 2 554 HIS 0.011 0.001 HIS 7 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (41733) covalent geometry : angle 0.83842 / 0.43 (56502) SS BOND : bond 0.00303 / 0.15 ( 3) SS BOND : angle 1.47612 / 0.67 ( 6) hydrogen bonds : bond 0.05373 / 3.53 ( 1089) hydrogen bonds : angle 6.60081 / 4.48 ( 3105) Misc. bond : bond 0.00540 / 0.26 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 683 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 214 SER cc_start: 0.8085 (m) cc_final: 0.7563 (p) REVERT: 2 271 SER cc_start: 0.6239 (OUTLIER) cc_final: 0.5821 (t) REVERT: 2 461 ARG cc_start: 0.6775 (ttp-110) cc_final: 0.6198 (ttm170) REVERT: 2 488 GLU cc_start: 0.4892 (mm-30) cc_final: 0.4228 (mm-30) REVERT: 2 605 LEU cc_start: 0.6841 (tp) cc_final: 0.6290 (tp) REVERT: 2 670 LYS cc_start: 0.3673 (pttp) cc_final: 0.3328 (mttp) REVERT: 2 752 GLU cc_start: 0.5236 (pt0) cc_final: 0.4580 (pt0) REVERT: 2 773 ARG cc_start: 0.4880 (ttm170) cc_final: 0.4571 (ttm170) REVERT: 3 253 PHE cc_start: 0.5994 (OUTLIER) cc_final: 0.5550 (t80) REVERT: 3 337 LEU cc_start: 0.4384 (tp) cc_final: 0.4079 (mt) REVERT: 3 348 GLN cc_start: 0.5734 (OUTLIER) cc_final: 0.5106 (tp40) REVERT: 3 418 HIS cc_start: 0.5617 (OUTLIER) cc_final: 0.5370 (m170) REVERT: 3 458 LYS cc_start: 0.6235 (tmmt) cc_final: 0.5474 (mmmt) REVERT: 3 462 GLU cc_start: 0.6791 (tp30) cc_final: 0.6260 (tp30) REVERT: 3 470 LEU cc_start: 0.6211 (mp) cc_final: 0.5839 (pp) REVERT: 4 211 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5495 (tp) REVERT: 4 513 ASP cc_start: 0.6750 (m-30) cc_final: 0.6401 (p0) REVERT: 4 524 TYR cc_start: 0.5316 (OUTLIER) cc_final: 0.5108 (m-80) REVERT: 4 590 HIS cc_start: 0.5929 (OUTLIER) cc_final: 0.5681 (m170) REVERT: 4 680 GLU cc_start: 0.1927 (pm20) cc_final: 0.0858 (mt-10) REVERT: 5 216 CYS cc_start: 0.5359 (OUTLIER) cc_final: 0.5083 (p) REVERT: 5 360 LYS cc_start: 0.3476 (mmtt) cc_final: 0.2854 (mmtp) REVERT: 5 379 ASP cc_start: 0.7278 (t0) cc_final: 0.7024 (t0) REVERT: 5 558 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.5021 (t80) REVERT: 6 129 ILE cc_start: 0.4029 (tt) cc_final: 0.3607 (mm) REVERT: 6 220 ILE cc_start: 0.6425 (OUTLIER) cc_final: 0.6082 (tp) REVERT: 6 284 LEU cc_start: 0.3544 (OUTLIER) cc_final: 0.2948 (pp) REVERT: 6 309 MET cc_start: 0.2323 (mtp) cc_final: 0.0443 (tmm) REVERT: 6 410 TYR cc_start: 0.4936 (OUTLIER) cc_final: 0.3517 (t80) REVERT: 6 457 MET cc_start: -0.2098 (mtt) cc_final: -0.2567 (mmt) REVERT: 7 83 GLU cc_start: 0.5157 (mm-30) cc_final: 0.4926 (pp20) REVERT: 7 203 VAL cc_start: 0.5820 (OUTLIER) cc_final: 0.5589 (t) REVERT: 7 215 LYS cc_start: 0.1417 (OUTLIER) cc_final: 0.0817 (tttp) REVERT: 7 281 MET cc_start: 0.6493 (mtm) cc_final: 0.6085 (mtp) REVERT: 7 282 ARG cc_start: 0.7587 (tmt-80) cc_final: 0.6940 (ttm-80) REVERT: 7 299 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: 7 419 MET cc_start: -0.0794 (ttp) cc_final: -0.3814 (mmt) REVERT: 7 494 ARG cc_start: 0.4191 (ptm-80) cc_final: 0.2893 (ttm170) REVERT: 7 560 ARG cc_start: 0.7442 (mtt180) cc_final: 0.7220 (mtt180) REVERT: A 53 MET cc_start: 0.4564 (mpp) cc_final: 0.3963 (mtm) REVERT: A 65 HIS cc_start: 0.7131 (m-70) cc_final: 0.6920 (m170) REVERT: A 304 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7479 (ttp80) REVERT: A 422 LYS cc_start: 0.4224 (mmtt) cc_final: 0.3968 (mmmt) REVERT: H 85 LEU cc_start: 0.7967 (pp) cc_final: 0.7597 (pp) REVERT: L 120 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7125 (mm) REVERT: N 82 LYS cc_start: 0.5491 (mppt) cc_final: 0.5074 (pttm) REVERT: N 151 TYR cc_start: 0.3013 (t80) cc_final: 0.2571 (t80) outliers start: 240 outliers final: 133 residues processed: 865 average time/residue: 0.2615 time to fit residues: 368.3653 Evaluate side-chains 752 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 602 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 554 TRP Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 568 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 640 SER Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 92 HIS Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 151 VAL Chi-restraints excluded: chain 3 residue 156 TYR Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 418 HIS Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 3 residue 647 TYR Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 478 ILE Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 645 ARG Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 685 ASP Chi-restraints excluded: chain 4 residue 757 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 117 HIS Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 332 LEU Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 414 SER Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 85 CYS Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 145 LEU Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 281 MET Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 609 THR Chi-restraints excluded: chain 7 residue 5 ASP Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 76 ILE Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 299 GLN Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 166 HIS Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 69 GLN Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 237 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 158 optimal weight: 0.3980 chunk 201 optimal weight: 3.9990 chunk 188 optimal weight: 0.0970 chunk 272 optimal weight: 6.9990 chunk 361 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 423 optimal weight: 8.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 436 GLN 2 616 ASN 2 666 HIS ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 743 HIS 3 438 ASN 3 622 HIS 4 192 ASN ** 4 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 620 ASN ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN L 147 ASN M 131 HIS M 164 ASN N 36 GLN ** N 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.271696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.258912 restraints weight = 73431.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.258701 restraints weight = 85747.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.259065 restraints weight = 70286.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.258944 restraints weight = 63206.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.259285 restraints weight = 56679.277| |-----------------------------------------------------------------------------| r_work (final): 0.5048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5392 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 41741 Z= 0.171 Angle : 0.818 13.606 56508 Z= 0.417 Chirality : 0.048 0.282 6362 Planarity : 0.006 0.065 7230 Dihedral : 11.773 138.182 5961 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.62 % Favored : 86.36 % Rotamer: Outliers : 5.64 % Allowed : 22.51 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.11), residues: 5000 helix: -1.59 (0.12), residues: 1642 sheet: -3.27 (0.19), residues: 541 loop : -3.42 (0.10), residues: 2817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 129 TYR 0.040 0.002 TYR H 129 PHE 0.025 0.002 PHE 7 77 TRP 0.036 0.002 TRP 2 554 HIS 0.012 0.002 HIS N 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (41733) covalent geometry : angle 0.81784 / 0.42 (56502) SS BOND : bond 0.00252 / 0.13 ( 3) SS BOND : angle 1.04667 / 0.48 ( 6) hydrogen bonds : bond 0.05011 / 3.30 ( 1089) hydrogen bonds : angle 6.30607 / 4.26 ( 3105) Misc. bond : bond 0.01378 / 0.66 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 651 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 2 212 MET cc_start: 0.7789 (mmm) cc_final: 0.6365 (mtp) REVERT: 2 271 SER cc_start: 0.6355 (OUTLIER) cc_final: 0.5964 (t) REVERT: 2 351 GLU cc_start: 0.4758 (pm20) cc_final: 0.4505 (tp30) REVERT: 2 461 ARG cc_start: 0.6900 (ttp-110) cc_final: 0.6022 (ttp80) REVERT: 2 488 GLU cc_start: 0.5240 (mm-30) cc_final: 0.4512 (mm-30) REVERT: 2 670 LYS cc_start: 0.3841 (pttp) cc_final: 0.3599 (mttp) REVERT: 2 752 GLU cc_start: 0.5414 (pt0) cc_final: 0.4749 (pt0) REVERT: 2 764 MET cc_start: 0.6203 (tpp) cc_final: 0.5827 (tpt) REVERT: 2 773 ARG cc_start: 0.4986 (ttm170) cc_final: 0.4599 (ttm170) REVERT: 3 65 ASN cc_start: 0.5708 (t0) cc_final: 0.5111 (t0) REVERT: 3 151 VAL cc_start: 0.7420 (OUTLIER) cc_final: 0.7128 (t) REVERT: 3 253 PHE cc_start: 0.6202 (OUTLIER) cc_final: 0.5797 (t80) REVERT: 3 348 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5302 (tp40) REVERT: 3 364 THR cc_start: 0.5553 (p) cc_final: 0.5216 (p) REVERT: 3 462 GLU cc_start: 0.6538 (tp30) cc_final: 0.5963 (tp30) REVERT: 3 470 LEU cc_start: 0.6267 (mp) cc_final: 0.5876 (pp) REVERT: 3 562 MET cc_start: 0.5646 (tmm) cc_final: 0.5384 (ttm) REVERT: 3 604 THR cc_start: 0.3958 (OUTLIER) cc_final: 0.3422 (m) REVERT: 4 173 MET cc_start: 0.6703 (mmm) cc_final: 0.6038 (mmp) REVERT: 4 211 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5476 (tp) REVERT: 4 513 ASP cc_start: 0.6818 (m-30) cc_final: 0.6567 (p0) REVERT: 4 590 HIS cc_start: 0.5884 (OUTLIER) cc_final: 0.5583 (m170) REVERT: 4 680 GLU cc_start: 0.1460 (pm20) cc_final: 0.0713 (mt-10) REVERT: 5 71 ASP cc_start: 0.7450 (p0) cc_final: 0.7223 (p0) REVERT: 5 210 MET cc_start: 0.6633 (mmp) cc_final: 0.6375 (mmp) REVERT: 5 216 CYS cc_start: 0.5712 (OUTLIER) cc_final: 0.5443 (p) REVERT: 5 307 ARG cc_start: 0.5174 (OUTLIER) cc_final: 0.4754 (pmt170) REVERT: 5 360 LYS cc_start: 0.3416 (mmtt) cc_final: 0.2724 (mmtp) REVERT: 5 417 LYS cc_start: 0.8044 (mptt) cc_final: 0.7688 (mptt) REVERT: 5 558 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.5968 (t80) REVERT: 5 588 MET cc_start: 0.6136 (tpp) cc_final: 0.5885 (tpp) REVERT: 6 129 ILE cc_start: 0.4042 (tt) cc_final: 0.3685 (mm) REVERT: 6 284 LEU cc_start: 0.3745 (OUTLIER) cc_final: 0.3029 (pp) REVERT: 6 309 MET cc_start: 0.2510 (mtp) cc_final: 0.0552 (tmm) REVERT: 6 410 TYR cc_start: 0.5229 (OUTLIER) cc_final: 0.3649 (t80) REVERT: 7 57 GLU cc_start: 0.6463 (mp0) cc_final: 0.6011 (tp30) REVERT: 7 80 VAL cc_start: 0.6469 (OUTLIER) cc_final: 0.6251 (t) REVERT: 7 203 VAL cc_start: 0.5692 (OUTLIER) cc_final: 0.5396 (t) REVERT: 7 215 LYS cc_start: 0.1702 (OUTLIER) cc_final: 0.0918 (tttp) REVERT: 7 256 MET cc_start: 0.6941 (tmm) cc_final: 0.6601 (mmm) REVERT: 7 281 MET cc_start: 0.6544 (mtm) cc_final: 0.6171 (mtp) REVERT: 7 282 ARG cc_start: 0.7625 (tmt-80) cc_final: 0.7084 (ttm-80) REVERT: 7 419 MET cc_start: -0.1009 (ttp) cc_final: -0.3954 (mmt) REVERT: 7 494 ARG cc_start: 0.4259 (ptm-80) cc_final: 0.3059 (ttm170) REVERT: A 53 MET cc_start: 0.4787 (mpp) cc_final: 0.4074 (mtm) REVERT: H 7 MET cc_start: 0.4345 (mtp) cc_final: 0.4041 (mmp) REVERT: L 120 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7395 (mm) REVERT: M 47 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5894 (pm20) outliers start: 250 outliers final: 156 residues processed: 844 average time/residue: 0.2625 time to fit residues: 361.1787 Evaluate side-chains 766 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 593 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 436 GLN Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 568 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 611 VAL Chi-restraints excluded: chain 2 residue 640 SER Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 2 residue 776 LEU Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 92 HIS Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 151 VAL Chi-restraints excluded: chain 3 residue 156 TYR Chi-restraints excluded: chain 3 residue 199 GLN Chi-restraints excluded: chain 3 residue 201 MET Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 400 VAL Chi-restraints excluded: chain 3 residue 441 CYS Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 559 VAL Chi-restraints excluded: chain 3 residue 604 THR Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 3 residue 647 TYR Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 478 ILE Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 685 ASP Chi-restraints excluded: chain 4 residue 757 LEU Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 117 HIS Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 425 VAL Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 640 LEU Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 106 VAL Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 565 LEU Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 76 ILE Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 489 ASN Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 166 HIS Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 164 ASN Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 174 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 276 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 430 optimal weight: 0.9980 chunk 344 optimal weight: 7.9990 chunk 219 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 267 HIS ** 2 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 503 ASN ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 743 HIS 2 762 ASN 2 796 GLN 3 260 ASN 4 188 ASN ** 4 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 735 GLN ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 115 HIS ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 564 ASN A 262 GLN A 444 GLN A 487 HIS ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5123 r_free = 0.5123 target = 0.267829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.253656 restraints weight = 73576.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.253095 restraints weight = 102644.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.254147 restraints weight = 83990.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.254265 restraints weight = 64142.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.254517 restraints weight = 59130.249| |-----------------------------------------------------------------------------| r_work (final): 0.4981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5548 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 41741 Z= 0.189 Angle : 0.838 15.182 56508 Z= 0.426 Chirality : 0.049 0.281 6362 Planarity : 0.006 0.067 7230 Dihedral : 11.725 137.633 5954 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.08 % Favored : 85.88 % Rotamer: Outliers : 5.87 % Allowed : 23.93 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.11), residues: 5000 helix: -1.52 (0.12), residues: 1641 sheet: -3.30 (0.19), residues: 564 loop : -3.41 (0.10), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 5 51 TYR 0.031 0.002 TYR 7 182 PHE 0.026 0.002 PHE 5 643 TRP 0.029 0.002 TRP 2 554 HIS 0.021 0.002 HIS N 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (41733) covalent geometry : angle 0.83821 / 0.43 (56502) SS BOND : bond 0.00308 / 0.15 ( 3) SS BOND : angle 1.23542 / 0.57 ( 6) hydrogen bonds : bond 0.05039 / 3.34 ( 1089) hydrogen bonds : angle 6.25232 / 4.23 ( 3105) Misc. bond : bond 0.00240 / 0.12 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 626 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. REVERT: 2 212 MET cc_start: 0.7884 (mmm) cc_final: 0.6662 (mtp) REVERT: 2 271 SER cc_start: 0.6527 (OUTLIER) cc_final: 0.6017 (t) REVERT: 2 351 GLU cc_start: 0.5070 (pm20) cc_final: 0.4649 (tp30) REVERT: 2 461 ARG cc_start: 0.6925 (ttp-110) cc_final: 0.6176 (ttp80) REVERT: 2 488 GLU cc_start: 0.5664 (mm-30) cc_final: 0.4978 (mm-30) REVERT: 2 587 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5259 (tm-30) REVERT: 2 670 LYS cc_start: 0.4532 (pttp) cc_final: 0.4046 (mttp) REVERT: 2 697 LEU cc_start: 0.4340 (OUTLIER) cc_final: 0.4054 (tt) REVERT: 2 752 GLU cc_start: 0.5730 (pt0) cc_final: 0.5046 (pt0) REVERT: 3 65 ASN cc_start: 0.5908 (t0) cc_final: 0.5372 (t0) REVERT: 3 121 MET cc_start: 0.6495 (mpp) cc_final: 0.4686 (ttt) REVERT: 3 155 LYS cc_start: 0.5991 (tptt) cc_final: 0.5491 (tttt) REVERT: 3 241 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5538 (mp) REVERT: 3 253 PHE cc_start: 0.6303 (OUTLIER) cc_final: 0.5847 (t80) REVERT: 3 265 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6535 (pp) REVERT: 3 348 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.5433 (tp40) REVERT: 3 364 THR cc_start: 0.5871 (p) cc_final: 0.5602 (p) REVERT: 3 462 GLU cc_start: 0.6756 (tp30) cc_final: 0.6037 (tp30) REVERT: 3 604 THR cc_start: 0.3550 (OUTLIER) cc_final: 0.3069 (m) REVERT: 4 211 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5650 (tp) REVERT: 4 466 ARG cc_start: 0.4133 (ppt170) cc_final: 0.3882 (ptt90) REVERT: 4 513 ASP cc_start: 0.6904 (m-30) cc_final: 0.6595 (p0) REVERT: 4 676 ARG cc_start: 0.1813 (pmt-80) cc_final: 0.1379 (ptm160) REVERT: 4 680 GLU cc_start: 0.1785 (pm20) cc_final: 0.0752 (mt-10) REVERT: 5 210 MET cc_start: 0.6769 (mmp) cc_final: 0.6439 (mmp) REVERT: 5 216 CYS cc_start: 0.6120 (OUTLIER) cc_final: 0.5861 (p) REVERT: 5 220 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.5738 (tm-30) REVERT: 5 245 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6835 (t0) REVERT: 5 307 ARG cc_start: 0.5220 (OUTLIER) cc_final: 0.4818 (pmt170) REVERT: 5 468 LYS cc_start: 0.8291 (mmtp) cc_final: 0.7973 (mmmt) REVERT: 5 558 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.5181 (t80) REVERT: 5 562 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7598 (mp) REVERT: 5 588 MET cc_start: 0.6023 (tpp) cc_final: 0.5806 (tpp) REVERT: 6 151 MET cc_start: 0.0100 (ttp) cc_final: -0.0165 (ttt) REVERT: 6 284 LEU cc_start: 0.3961 (OUTLIER) cc_final: 0.3277 (pp) REVERT: 6 291 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6373 (tt) REVERT: 6 309 MET cc_start: 0.2617 (mtp) cc_final: 0.0453 (tmm) REVERT: 6 410 TYR cc_start: 0.5511 (OUTLIER) cc_final: 0.3913 (t80) REVERT: 7 57 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6104 (tp30) REVERT: 7 215 LYS cc_start: 0.1823 (OUTLIER) cc_final: 0.0809 (tttp) REVERT: 7 281 MET cc_start: 0.6743 (mtm) cc_final: 0.6345 (mtp) REVERT: 7 369 MET cc_start: 0.3674 (ptm) cc_final: 0.3150 (ptt) REVERT: 7 419 MET cc_start: -0.1318 (ttp) cc_final: -0.4087 (mmt) REVERT: 7 494 ARG cc_start: 0.4401 (ptm-80) cc_final: 0.3174 (ttm170) REVERT: A 53 MET cc_start: 0.4959 (mpp) cc_final: 0.4282 (mtm) REVERT: A 398 GLU cc_start: 0.5567 (tt0) cc_final: 0.5249 (tt0) REVERT: H 7 MET cc_start: 0.4912 (mtp) cc_final: 0.4003 (mmp) REVERT: L 21 PHE cc_start: 0.4060 (OUTLIER) cc_final: 0.3662 (m-80) REVERT: M 47 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6110 (pm20) REVERT: N 77 MET cc_start: 0.6368 (tmm) cc_final: 0.6145 (ptp) outliers start: 260 outliers final: 173 residues processed: 836 average time/residue: 0.2551 time to fit residues: 350.8343 Evaluate side-chains 780 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 585 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 239 GLN Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 294 LEU Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 568 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 587 GLU Chi-restraints excluded: chain 2 residue 611 VAL Chi-restraints excluded: chain 2 residue 640 SER Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 697 LEU Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 92 HIS Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 118 LEU Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 156 TYR Chi-restraints excluded: chain 3 residue 210 LEU Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 234 ILE Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 400 VAL Chi-restraints excluded: chain 3 residue 417 ILE Chi-restraints excluded: chain 3 residue 418 HIS Chi-restraints excluded: chain 3 residue 441 CYS Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 604 THR Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 3 residue 647 TYR Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 189 ILE Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 230 ILE Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 685 ASP Chi-restraints excluded: chain 4 residue 712 LEU Chi-restraints excluded: chain 4 residue 757 LEU Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 332 LEU Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 565 LEU Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 57 GLU Chi-restraints excluded: chain 7 residue 76 ILE Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 185 ASP Chi-restraints excluded: chain 7 residue 205 ASP Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 340 LEU Chi-restraints excluded: chain 7 residue 350 VAL Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 387 LYS Chi-restraints excluded: chain 7 residue 421 ASP Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 489 ASN Chi-restraints excluded: chain 7 residue 551 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 166 HIS Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 160 MET Chi-restraints excluded: chain N residue 174 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 19 optimal weight: 0.1980 chunk 402 optimal weight: 0.5980 chunk 485 optimal weight: 0.0970 chunk 436 optimal weight: 0.9980 chunk 494 optimal weight: 0.9980 chunk 459 optimal weight: 0.9980 chunk 468 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 199 GLN 4 485 GLN 4 656 GLN ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 595 GLN 6 79 HIS ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 42 HIS 7 248 HIS 7 266 GLN ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS H 109 GLN ** N 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 214 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5153 r_free = 0.5153 target = 0.271725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.257825 restraints weight = 73487.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.257312 restraints weight = 97567.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.258307 restraints weight = 86143.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.258163 restraints weight = 65303.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.258559 restraints weight = 59594.225| |-----------------------------------------------------------------------------| r_work (final): 0.5040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5429 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 41741 Z= 0.144 Angle : 0.784 14.282 56508 Z= 0.394 Chirality : 0.047 0.338 6362 Planarity : 0.005 0.068 7230 Dihedral : 11.491 137.082 5951 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.22 % Favored : 86.76 % Rotamer: Outliers : 5.35 % Allowed : 24.86 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.11), residues: 5000 helix: -1.29 (0.12), residues: 1641 sheet: -3.14 (0.19), residues: 552 loop : -3.31 (0.10), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 2 773 TYR 0.025 0.002 TYR 5 585 PHE 0.033 0.002 PHE M 101 TRP 0.022 0.002 TRP 2 554 HIS 0.015 0.001 HIS 6 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (41733) covalent geometry : angle 0.78352 / 0.39 (56502) SS BOND : bond 0.00097 / 0.05 ( 3) SS BOND : angle 0.78674 / 0.39 ( 6) hydrogen bonds : bond 0.04605 / 3.03 ( 1089) hydrogen bonds : angle 6.06875 / 4.10 ( 3105) Misc. bond : bond 0.00112 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 636 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 2 212 MET cc_start: 0.7559 (mmm) cc_final: 0.6467 (mtp) REVERT: 2 271 SER cc_start: 0.6436 (OUTLIER) cc_final: 0.6085 (t) REVERT: 2 461 ARG cc_start: 0.6977 (ttp-110) cc_final: 0.6099 (ttp80) REVERT: 2 488 GLU cc_start: 0.5335 (mm-30) cc_final: 0.4675 (mm-30) REVERT: 2 587 GLU cc_start: 0.5884 (OUTLIER) cc_final: 0.5411 (tm-30) REVERT: 2 605 LEU cc_start: 0.6122 (tp) cc_final: 0.5504 (tp) REVERT: 2 697 LEU cc_start: 0.4407 (OUTLIER) cc_final: 0.4117 (tt) REVERT: 2 720 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7685 (tt) REVERT: 2 752 GLU cc_start: 0.5316 (pt0) cc_final: 0.4556 (pt0) REVERT: 3 65 ASN cc_start: 0.5701 (t0) cc_final: 0.5260 (t0) REVERT: 3 121 MET cc_start: 0.6496 (mpp) cc_final: 0.4561 (ttt) REVERT: 3 155 LYS cc_start: 0.6199 (tptt) cc_final: 0.5708 (tttt) REVERT: 3 253 PHE cc_start: 0.6309 (OUTLIER) cc_final: 0.5808 (t80) REVERT: 3 348 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.5363 (tp40) REVERT: 3 364 THR cc_start: 0.4959 (p) cc_final: 0.4572 (p) REVERT: 3 462 GLU cc_start: 0.6696 (tp30) cc_final: 0.5885 (tp30) REVERT: 3 604 THR cc_start: 0.3327 (OUTLIER) cc_final: 0.2881 (m) REVERT: 4 173 MET cc_start: 0.6675 (mmm) cc_final: 0.6033 (mmp) REVERT: 4 211 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5424 (tp) REVERT: 4 466 ARG cc_start: 0.3797 (ppt170) cc_final: 0.3541 (ptt90) REVERT: 4 480 LYS cc_start: 0.5973 (mmtp) cc_final: 0.5741 (mmtt) REVERT: 4 676 ARG cc_start: 0.1691 (pmt-80) cc_final: 0.1303 (ptm160) REVERT: 4 680 GLU cc_start: 0.1831 (pm20) cc_final: 0.0853 (mt-10) REVERT: 5 210 MET cc_start: 0.6757 (mmp) cc_final: 0.6369 (mmp) REVERT: 5 216 CYS cc_start: 0.5811 (OUTLIER) cc_final: 0.5609 (p) REVERT: 5 245 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6897 (t0) REVERT: 5 558 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.5290 (t80) REVERT: 5 562 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7427 (mp) REVERT: 6 284 LEU cc_start: 0.3869 (OUTLIER) cc_final: 0.3196 (pp) REVERT: 6 309 MET cc_start: 0.2636 (mtp) cc_final: 0.0346 (tmm) REVERT: 6 410 TYR cc_start: 0.5222 (OUTLIER) cc_final: 0.3732 (t80) REVERT: 6 584 HIS cc_start: 0.5143 (m90) cc_final: 0.4818 (t-170) REVERT: 6 634 GLU cc_start: 0.4088 (pm20) cc_final: 0.3797 (pm20) REVERT: 7 57 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6107 (tp30) REVERT: 7 182 TYR cc_start: 0.2982 (OUTLIER) cc_final: 0.2685 (m-80) REVERT: 7 210 ASP cc_start: 0.5325 (t0) cc_final: 0.4038 (m-30) REVERT: 7 215 LYS cc_start: 0.1639 (OUTLIER) cc_final: 0.0834 (tttp) REVERT: 7 281 MET cc_start: 0.6507 (mtm) cc_final: 0.6169 (mtp) REVERT: 7 419 MET cc_start: -0.1127 (ttp) cc_final: -0.4047 (mmt) REVERT: 7 494 ARG cc_start: 0.4430 (ptm-80) cc_final: 0.3253 (ttm170) REVERT: A 53 MET cc_start: 0.4674 (mpp) cc_final: 0.3985 (mtm) REVERT: A 398 GLU cc_start: 0.5564 (tt0) cc_final: 0.5346 (tt0) REVERT: A 507 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.5385 (mp) REVERT: H 7 MET cc_start: 0.4913 (mtp) cc_final: 0.4093 (mmp) REVERT: L 18 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7778 (mt) REVERT: L 120 ILE cc_start: 0.8294 (tp) cc_final: 0.7565 (mm) REVERT: M 47 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.5751 (pp20) REVERT: N 30 MET cc_start: 0.2244 (mmt) cc_final: 0.2003 (mmm) outliers start: 237 outliers final: 160 residues processed: 819 average time/residue: 0.2579 time to fit residues: 345.6577 Evaluate side-chains 752 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 572 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 217 VAL Chi-restraints excluded: chain 2 residue 239 GLN Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 294 LEU Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 568 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 587 GLU Chi-restraints excluded: chain 2 residue 611 VAL Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 697 LEU Chi-restraints excluded: chain 2 residue 720 ILE Chi-restraints excluded: chain 2 residue 744 ILE Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 57 GLN Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 92 HIS Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 156 TYR Chi-restraints excluded: chain 3 residue 199 GLN Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 418 HIS Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 531 GLU Chi-restraints excluded: chain 3 residue 559 VAL Chi-restraints excluded: chain 3 residue 567 HIS Chi-restraints excluded: chain 3 residue 604 THR Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 189 ILE Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 230 ILE Chi-restraints excluded: chain 4 residue 282 MET Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 685 ASP Chi-restraints excluded: chain 4 residue 757 LEU Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 117 HIS Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 208 PHE Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 332 LEU Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 481 VAL Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 106 VAL Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 327 HIS Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 382 ILE Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 565 LEU Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 57 GLU Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 182 TYR Chi-restraints excluded: chain 7 residue 185 ASP Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 340 LEU Chi-restraints excluded: chain 7 residue 350 VAL Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 387 LYS Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 166 HIS Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 160 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 333 optimal weight: 10.0000 chunk 436 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 351 optimal weight: 9.9990 chunk 322 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 212 optimal weight: 0.0770 chunk 438 optimal weight: 2.9990 chunk 314 optimal weight: 0.4980 chunk 239 optimal weight: 2.9990 chunk 269 optimal weight: 0.0270 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 666 HIS ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 188 ASN 4 533 GLN 4 631 ASN ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 134 GLN ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 396 GLN 7 42 HIS ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN ** N 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 HIS ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5155 r_free = 0.5155 target = 0.272045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.5039 r_free = 0.5039 target = 0.258920 restraints weight = 73528.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.258592 restraints weight = 86938.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5022 r_free = 0.5022 target = 0.258230 restraints weight = 64479.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.258127 restraints weight = 55966.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.258086 restraints weight = 53924.498| |-----------------------------------------------------------------------------| r_work (final): 0.5034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5456 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 41741 Z= 0.146 Angle : 0.782 12.809 56508 Z= 0.392 Chirality : 0.047 0.201 6362 Planarity : 0.005 0.070 7230 Dihedral : 11.306 138.063 5947 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.88 % Favored : 87.10 % Rotamer: Outliers : 5.12 % Allowed : 25.90 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.11), residues: 5000 helix: -1.15 (0.12), residues: 1653 sheet: -3.06 (0.19), residues: 566 loop : -3.22 (0.11), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG H 76 TYR 0.028 0.002 TYR 5 585 PHE 0.032 0.002 PHE 4 248 TRP 0.018 0.002 TRP M 170 HIS 0.011 0.001 HIS 7 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (41733) covalent geometry : angle 0.78197 / 0.39 (56502) SS BOND : bond 0.00233 / 0.12 ( 3) SS BOND : angle 0.97511 / 0.46 ( 6) hydrogen bonds : bond 0.04487 / 2.95 ( 1089) hydrogen bonds : angle 5.90159 / 3.99 ( 3105) Misc. bond : bond 0.00085 / 0.04 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 627 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 212 MET cc_start: 0.7478 (mmm) cc_final: 0.6523 (mtp) REVERT: 2 271 SER cc_start: 0.6445 (OUTLIER) cc_final: 0.6131 (t) REVERT: 2 461 ARG cc_start: 0.6941 (ttp-110) cc_final: 0.6078 (ttp80) REVERT: 2 466 MET cc_start: 0.0394 (ttm) cc_final: -0.0299 (ttm) REVERT: 2 488 GLU cc_start: 0.5477 (mm-30) cc_final: 0.4885 (mm-30) REVERT: 2 587 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5552 (tm-30) REVERT: 2 605 LEU cc_start: 0.6323 (tp) cc_final: 0.5828 (tp) REVERT: 2 697 LEU cc_start: 0.4454 (OUTLIER) cc_final: 0.4206 (tt) REVERT: 2 720 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7702 (tt) REVERT: 2 752 GLU cc_start: 0.5411 (pt0) cc_final: 0.4714 (pt0) REVERT: 3 65 ASN cc_start: 0.5789 (t0) cc_final: 0.5304 (t0) REVERT: 3 121 MET cc_start: 0.6408 (mpp) cc_final: 0.4523 (ttt) REVERT: 3 155 LYS cc_start: 0.6284 (tptt) cc_final: 0.5808 (tttt) REVERT: 3 253 PHE cc_start: 0.6179 (OUTLIER) cc_final: 0.5747 (t80) REVERT: 3 348 GLN cc_start: 0.6492 (OUTLIER) cc_final: 0.5337 (tp40) REVERT: 3 462 GLU cc_start: 0.6705 (tp30) cc_final: 0.6138 (tp30) REVERT: 3 466 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5998 (mp) REVERT: 3 604 THR cc_start: 0.3358 (OUTLIER) cc_final: 0.2926 (m) REVERT: 4 173 MET cc_start: 0.6889 (mmm) cc_final: 0.6411 (mmp) REVERT: 4 466 ARG cc_start: 0.4426 (ppt170) cc_final: 0.4211 (ptt90) REVERT: 4 676 ARG cc_start: 0.1861 (pmt-80) cc_final: 0.1340 (ptm160) REVERT: 4 680 GLU cc_start: 0.2034 (pm20) cc_final: 0.0982 (mt-10) REVERT: 5 210 MET cc_start: 0.6498 (mmp) cc_final: 0.6157 (mmp) REVERT: 5 220 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.5717 (tm-30) REVERT: 5 245 ASP cc_start: 0.7128 (OUTLIER) cc_final: 0.6810 (t0) REVERT: 5 346 ILE cc_start: 0.6364 (OUTLIER) cc_final: 0.6124 (mt) REVERT: 5 558 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.5210 (t80) REVERT: 5 562 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7538 (mp) REVERT: 6 284 LEU cc_start: 0.3721 (OUTLIER) cc_final: 0.3088 (pp) REVERT: 6 309 MET cc_start: 0.2672 (mtp) cc_final: 0.0335 (tmm) REVERT: 6 410 TYR cc_start: 0.5255 (OUTLIER) cc_final: 0.3783 (t80) REVERT: 7 57 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6139 (tp30) REVERT: 7 210 ASP cc_start: 0.5414 (t0) cc_final: 0.4324 (m-30) REVERT: 7 215 LYS cc_start: 0.1711 (OUTLIER) cc_final: 0.0856 (tttp) REVERT: 7 248 HIS cc_start: 0.6564 (t70) cc_final: 0.6144 (t70) REVERT: 7 281 MET cc_start: 0.6397 (mtm) cc_final: 0.6064 (mtp) REVERT: 7 419 MET cc_start: -0.0979 (ttp) cc_final: -0.3946 (mmt) REVERT: 7 494 ARG cc_start: 0.4443 (ptm-80) cc_final: 0.3263 (ttm170) REVERT: A 53 MET cc_start: 0.4809 (mpp) cc_final: 0.4111 (mtm) REVERT: A 398 GLU cc_start: 0.5777 (tt0) cc_final: 0.5382 (tt0) REVERT: A 507 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.5565 (mp) REVERT: L 18 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7842 (mt) REVERT: L 120 ILE cc_start: 0.8331 (tp) cc_final: 0.7592 (mm) REVERT: M 24 GLU cc_start: 0.6279 (mp0) cc_final: 0.5895 (pt0) REVERT: M 84 VAL cc_start: 0.6793 (m) cc_final: 0.6508 (p) REVERT: N 30 MET cc_start: 0.2295 (mmt) cc_final: 0.2093 (mmm) outliers start: 227 outliers final: 154 residues processed: 803 average time/residue: 0.2579 time to fit residues: 339.1865 Evaluate side-chains 747 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 574 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 239 GLN Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 397 LEU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 568 VAL Chi-restraints excluded: chain 2 residue 587 GLU Chi-restraints excluded: chain 2 residue 611 VAL Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 697 LEU Chi-restraints excluded: chain 2 residue 720 ILE Chi-restraints excluded: chain 2 residue 744 ILE Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 57 GLN Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 116 ILE Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 156 TYR Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 531 GLU Chi-restraints excluded: chain 3 residue 604 THR Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 189 ILE Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 230 ILE Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 208 PHE Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 346 ILE Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 481 VAL Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 69 LEU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 106 VAL Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 327 HIS Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 565 LEU Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 57 GLU Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 340 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 399 VAL Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 160 MET Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 28 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 chunk 434 optimal weight: 6.9990 chunk 353 optimal weight: 6.9990 chunk 151 optimal weight: 0.0970 chunk 295 optimal weight: 0.5980 chunk 120 optimal weight: 7.9990 chunk 395 optimal weight: 2.9990 chunk 440 optimal weight: 0.6980 chunk 269 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 436 GLN 2 586 HIS ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 672 HIS 2 754 HIS 4 635 ASN ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 584 HIS 7 248 HIS 7 266 GLN 7 374 ASN 7 376 ASN ** 7 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.269804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.256654 restraints weight = 73365.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.256653 restraints weight = 83941.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.255101 restraints weight = 56602.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.254874 restraints weight = 62023.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.255066 restraints weight = 58097.673| |-----------------------------------------------------------------------------| r_work (final): 0.4977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 41741 Z= 0.157 Angle : 0.791 12.691 56508 Z= 0.396 Chirality : 0.047 0.255 6362 Planarity : 0.005 0.070 7230 Dihedral : 11.230 137.115 5941 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.20 % Favored : 86.78 % Rotamer: Outliers : 5.28 % Allowed : 26.21 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.11), residues: 5000 helix: -1.09 (0.12), residues: 1662 sheet: -2.91 (0.20), residues: 562 loop : -3.23 (0.10), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 76 TYR 0.035 0.002 TYR 7 182 PHE 0.026 0.002 PHE 5 643 TRP 0.019 0.002 TRP 2 554 HIS 0.016 0.001 HIS 6 584 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (41733) covalent geometry : angle 0.79062 / 0.40 (56502) SS BOND : bond 0.00234 / 0.12 ( 3) SS BOND : angle 0.92153 / 0.45 ( 6) hydrogen bonds : bond 0.04532 / 2.97 ( 1089) hydrogen bonds : angle 5.83131 / 3.93 ( 3105) Misc. bond : bond 0.00123 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 610 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 212 MET cc_start: 0.7456 (mmm) cc_final: 0.6467 (mtp) REVERT: 2 271 SER cc_start: 0.6513 (OUTLIER) cc_final: 0.6113 (t) REVERT: 2 290 LEU cc_start: 0.2220 (OUTLIER) cc_final: 0.1880 (mp) REVERT: 2 461 ARG cc_start: 0.6968 (ttp-110) cc_final: 0.6121 (ttp80) REVERT: 2 466 MET cc_start: 0.0748 (ttm) cc_final: 0.0028 (ttm) REVERT: 2 488 GLU cc_start: 0.5997 (mm-30) cc_final: 0.5374 (mm-30) REVERT: 2 587 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5918 (tm-30) REVERT: 2 605 LEU cc_start: 0.6481 (tp) cc_final: 0.5930 (tp) REVERT: 2 715 ILE cc_start: 0.3017 (OUTLIER) cc_final: 0.2812 (mm) REVERT: 2 720 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7669 (tt) REVERT: 2 727 LEU cc_start: 0.2408 (tt) cc_final: 0.1809 (mp) REVERT: 2 752 GLU cc_start: 0.5750 (pt0) cc_final: 0.4913 (pt0) REVERT: 3 65 ASN cc_start: 0.5982 (t0) cc_final: 0.5348 (t0) REVERT: 3 155 LYS cc_start: 0.6291 (tptt) cc_final: 0.5798 (tttt) REVERT: 3 253 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.5856 (t80) REVERT: 3 286 LYS cc_start: 0.4715 (tptt) cc_final: 0.4509 (tptp) REVERT: 3 462 GLU cc_start: 0.6980 (tp30) cc_final: 0.6213 (tp30) REVERT: 3 603 ARG cc_start: 0.6166 (tpt-90) cc_final: 0.5961 (tpt90) REVERT: 3 604 THR cc_start: 0.3573 (OUTLIER) cc_final: 0.3308 (m) REVERT: 4 173 MET cc_start: 0.6676 (mmm) cc_final: 0.6395 (mmp) REVERT: 4 189 ILE cc_start: 0.1557 (OUTLIER) cc_final: 0.1078 (tt) REVERT: 4 480 LYS cc_start: 0.5920 (mmtt) cc_final: 0.5235 (mmtp) REVERT: 4 676 ARG cc_start: 0.2399 (pmt-80) cc_final: 0.1596 (ptm160) REVERT: 4 680 GLU cc_start: 0.2080 (OUTLIER) cc_final: 0.0964 (mt-10) REVERT: 5 210 MET cc_start: 0.6792 (mmp) cc_final: 0.6455 (mmp) REVERT: 5 220 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.5800 (tm-30) REVERT: 5 245 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6687 (t0) REVERT: 5 307 ARG cc_start: 0.5294 (OUTLIER) cc_final: 0.4857 (pmt170) REVERT: 5 558 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.5061 (t80) REVERT: 5 562 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7708 (mp) REVERT: 6 284 LEU cc_start: 0.3750 (OUTLIER) cc_final: 0.3115 (pp) REVERT: 6 309 MET cc_start: 0.2804 (mtp) cc_final: 0.0488 (tmm) REVERT: 6 410 TYR cc_start: 0.5740 (OUTLIER) cc_final: 0.3991 (t80) REVERT: 7 57 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6114 (tp30) REVERT: 7 210 ASP cc_start: 0.5575 (t0) cc_final: 0.4435 (m-30) REVERT: 7 215 LYS cc_start: 0.1678 (OUTLIER) cc_final: 0.0780 (tttm) REVERT: 7 266 GLN cc_start: 0.5098 (OUTLIER) cc_final: 0.4800 (mm-40) REVERT: 7 281 MET cc_start: 0.6660 (mtm) cc_final: 0.6223 (mtp) REVERT: 7 419 MET cc_start: -0.1325 (ttp) cc_final: -0.3960 (mmt) REVERT: 7 494 ARG cc_start: 0.4528 (ptm-80) cc_final: 0.3334 (ttm170) REVERT: A 53 MET cc_start: 0.5125 (mpp) cc_final: 0.4374 (mtm) REVERT: A 398 GLU cc_start: 0.5760 (tt0) cc_final: 0.5469 (tt0) REVERT: A 507 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.5730 (mp) REVERT: H 7 MET cc_start: 0.4218 (mtp) cc_final: 0.3744 (mtp) REVERT: H 130 MET cc_start: 0.5267 (mmm) cc_final: 0.5030 (mmt) REVERT: L 18 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7918 (mt) REVERT: L 120 ILE cc_start: 0.8345 (tp) cc_final: 0.7743 (mm) REVERT: M 24 GLU cc_start: 0.6575 (mp0) cc_final: 0.6279 (pt0) REVERT: M 84 VAL cc_start: 0.7026 (m) cc_final: 0.6718 (p) outliers start: 234 outliers final: 174 residues processed: 791 average time/residue: 0.2574 time to fit residues: 334.4337 Evaluate side-chains 767 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 572 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 217 VAL Chi-restraints excluded: chain 2 residue 239 GLN Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 397 LEU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 436 GLN Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 568 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 587 GLU Chi-restraints excluded: chain 2 residue 611 VAL Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 715 ILE Chi-restraints excluded: chain 2 residue 720 ILE Chi-restraints excluded: chain 2 residue 744 ILE Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 57 GLN Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 116 ILE Chi-restraints excluded: chain 3 residue 118 LEU Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 156 TYR Chi-restraints excluded: chain 3 residue 210 LEU Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 417 ILE Chi-restraints excluded: chain 3 residue 418 HIS Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 531 GLU Chi-restraints excluded: chain 3 residue 567 HIS Chi-restraints excluded: chain 3 residue 604 THR Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 189 ILE Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 230 ILE Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 432 LEU Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 646 PHE Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 208 PHE Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 332 LEU Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 481 VAL Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 69 LEU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 106 VAL Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 179 CYS Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 327 HIS Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 382 ILE Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 518 ILE Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 565 LEU Chi-restraints excluded: chain 6 residue 584 HIS Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 57 GLU Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 185 ASP Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 266 GLN Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 340 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 551 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 160 MET Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 285 optimal weight: 7.9990 chunk 393 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 488 optimal weight: 0.4980 chunk 350 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 353 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 586 HIS ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 107 HIS ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 266 GLN 7 376 ASN ** 7 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 HIS ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.268763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.254374 restraints weight = 73676.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.253657 restraints weight = 100883.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.254824 restraints weight = 85517.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4992 r_free = 0.4992 target = 0.254722 restraints weight = 66035.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.254988 restraints weight = 60627.294| |-----------------------------------------------------------------------------| r_work (final): 0.4985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41741 Z= 0.160 Angle : 0.806 12.207 56508 Z= 0.404 Chirality : 0.047 0.265 6362 Planarity : 0.005 0.072 7230 Dihedral : 11.160 134.102 5936 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.28 % Favored : 86.70 % Rotamer: Outliers : 5.03 % Allowed : 26.53 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.11), residues: 5000 helix: -1.00 (0.13), residues: 1654 sheet: -2.90 (0.19), residues: 574 loop : -3.22 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 76 TYR 0.024 0.002 TYR 3 16 PHE 0.029 0.002 PHE 2 282 TRP 0.025 0.002 TRP 2 554 HIS 0.032 0.002 HIS 6 584 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (41733) covalent geometry : angle 0.80637 / 0.40 (56502) SS BOND : bond 0.00256 / 0.13 ( 3) SS BOND : angle 0.89987 / 0.45 ( 6) hydrogen bonds : bond 0.04466 / 2.94 ( 1089) hydrogen bonds : angle 5.81093 / 3.91 ( 3105) Misc. bond : bond 0.00115 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 588 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 212 MET cc_start: 0.7400 (mmm) cc_final: 0.6521 (mtp) REVERT: 2 271 SER cc_start: 0.6458 (OUTLIER) cc_final: 0.6043 (t) REVERT: 2 290 LEU cc_start: 0.2724 (OUTLIER) cc_final: 0.2330 (mt) REVERT: 2 364 GLN cc_start: 0.5147 (OUTLIER) cc_final: 0.4938 (tt0) REVERT: 2 383 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7426 (mp) REVERT: 2 461 ARG cc_start: 0.7003 (ttp-110) cc_final: 0.6149 (ttp80) REVERT: 2 466 MET cc_start: 0.0408 (ttm) cc_final: -0.0190 (ttm) REVERT: 2 488 GLU cc_start: 0.6101 (mm-30) cc_final: 0.5418 (mm-30) REVERT: 2 587 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.6037 (tm-30) REVERT: 2 605 LEU cc_start: 0.6459 (tp) cc_final: 0.5991 (tp) REVERT: 2 720 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7683 (tt) REVERT: 2 727 LEU cc_start: 0.2943 (tt) cc_final: 0.2356 (mp) REVERT: 2 752 GLU cc_start: 0.5881 (pt0) cc_final: 0.5075 (pt0) REVERT: 3 65 ASN cc_start: 0.6002 (t0) cc_final: 0.5393 (t0) REVERT: 3 91 MET cc_start: 0.7518 (mpp) cc_final: 0.7090 (mpp) REVERT: 3 155 LYS cc_start: 0.6292 (tptt) cc_final: 0.5778 (tttt) REVERT: 3 253 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.6060 (t80) REVERT: 3 462 GLU cc_start: 0.6934 (tp30) cc_final: 0.6191 (tp30) REVERT: 3 604 THR cc_start: 0.3432 (OUTLIER) cc_final: 0.3171 (m) REVERT: 4 173 MET cc_start: 0.6689 (mmm) cc_final: 0.6422 (mmp) REVERT: 4 189 ILE cc_start: 0.1230 (OUTLIER) cc_final: 0.0764 (tt) REVERT: 4 480 LYS cc_start: 0.6079 (mmtt) cc_final: 0.5437 (mmtp) REVERT: 4 676 ARG cc_start: 0.2397 (pmt-80) cc_final: 0.1641 (ptm160) REVERT: 4 680 GLU cc_start: 0.2384 (OUTLIER) cc_final: 0.1281 (mt-10) REVERT: 5 210 MET cc_start: 0.6796 (mmp) cc_final: 0.6464 (mmp) REVERT: 5 220 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.5742 (tm-30) REVERT: 5 245 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6778 (t0) REVERT: 5 307 ARG cc_start: 0.5334 (OUTLIER) cc_final: 0.4903 (pmt170) REVERT: 5 417 LYS cc_start: 0.7942 (mptt) cc_final: 0.7660 (mttt) REVERT: 5 558 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.5179 (t80) REVERT: 5 562 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7731 (mp) REVERT: 6 284 LEU cc_start: 0.3740 (OUTLIER) cc_final: 0.3085 (pp) REVERT: 6 291 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6196 (tt) REVERT: 6 309 MET cc_start: 0.2839 (mtp) cc_final: 0.0805 (tmm) REVERT: 6 410 TYR cc_start: 0.5755 (OUTLIER) cc_final: 0.4009 (t80) REVERT: 7 57 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6048 (tp30) REVERT: 7 210 ASP cc_start: 0.5465 (t0) cc_final: 0.4388 (m-30) REVERT: 7 215 LYS cc_start: 0.1826 (OUTLIER) cc_final: 0.0874 (mtpt) REVERT: 7 281 MET cc_start: 0.6671 (mtm) cc_final: 0.6234 (mtp) REVERT: 7 369 MET cc_start: 0.4124 (ptm) cc_final: 0.3645 (ptt) REVERT: 7 419 MET cc_start: -0.1158 (ttp) cc_final: -0.3832 (mmt) REVERT: 7 494 ARG cc_start: 0.4553 (ptm-80) cc_final: 0.3356 (ttm170) REVERT: A 53 MET cc_start: 0.5219 (mpp) cc_final: 0.4405 (mtm) REVERT: A 101 HIS cc_start: 0.5687 (OUTLIER) cc_final: 0.4936 (m90) REVERT: A 398 GLU cc_start: 0.5834 (tt0) cc_final: 0.5577 (tt0) REVERT: A 507 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.5798 (mp) REVERT: H 130 MET cc_start: 0.5396 (mmm) cc_final: 0.5188 (mmt) REVERT: L 18 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7956 (mt) REVERT: L 120 ILE cc_start: 0.8376 (tp) cc_final: 0.7752 (mm) REVERT: M 24 GLU cc_start: 0.6674 (mp0) cc_final: 0.6415 (pt0) REVERT: M 84 VAL cc_start: 0.6881 (m) cc_final: 0.6641 (p) outliers start: 223 outliers final: 175 residues processed: 760 average time/residue: 0.2518 time to fit residues: 316.1587 Evaluate side-chains 764 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 566 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 217 VAL Chi-restraints excluded: chain 2 residue 239 GLN Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 364 GLN Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 397 LEU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 404 THR Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 448 THR Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 568 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 587 GLU Chi-restraints excluded: chain 2 residue 611 VAL Chi-restraints excluded: chain 2 residue 640 SER Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 720 ILE Chi-restraints excluded: chain 2 residue 744 ILE Chi-restraints excluded: chain 2 residue 787 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 57 GLN Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 116 ILE Chi-restraints excluded: chain 3 residue 118 LEU Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 156 TYR Chi-restraints excluded: chain 3 residue 210 LEU Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 312 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 417 ILE Chi-restraints excluded: chain 3 residue 418 HIS Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 531 GLU Chi-restraints excluded: chain 3 residue 567 HIS Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 604 THR Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 189 ILE Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 230 ILE Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 432 LEU Chi-restraints excluded: chain 4 residue 570 ASN Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 646 PHE Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 208 PHE Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 481 VAL Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 69 LEU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 106 VAL Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 327 HIS Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 382 ILE Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 518 ILE Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 555 VAL Chi-restraints excluded: chain 6 residue 565 LEU Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 42 HIS Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 57 GLU Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 185 ASP Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 340 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 551 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 160 MET Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 408 optimal weight: 0.6980 chunk 370 optimal weight: 1.9990 chunk 279 optimal weight: 0.0050 chunk 369 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 293 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 431 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 586 HIS ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 288 ASN ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 584 HIS 7 266 GLN 7 376 ASN H 109 GLN ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5138 r_free = 0.5138 target = 0.270341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.256520 restraints weight = 73103.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.255988 restraints weight = 91502.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.255194 restraints weight = 64534.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.255087 restraints weight = 61446.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.255114 restraints weight = 59396.935| |-----------------------------------------------------------------------------| r_work (final): 0.4981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 41741 Z= 0.145 Angle : 0.791 12.616 56508 Z= 0.394 Chirality : 0.047 0.265 6362 Planarity : 0.005 0.071 7230 Dihedral : 11.062 132.347 5936 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.92 % Favored : 87.06 % Rotamer: Outliers : 4.60 % Allowed : 27.23 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.11), residues: 5000 helix: -0.89 (0.13), residues: 1647 sheet: -2.75 (0.20), residues: 574 loop : -3.17 (0.11), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 5 584 TYR 0.023 0.002 TYR M 107 PHE 0.026 0.002 PHE 5 643 TRP 0.028 0.002 TRP A 223 HIS 0.016 0.001 HIS 7 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (41733) covalent geometry : angle 0.79112 / 0.39 (56502) SS BOND : bond 0.00212 / 0.11 ( 3) SS BOND : angle 0.72857 / 0.37 ( 6) hydrogen bonds : bond 0.04309 / 2.83 ( 1089) hydrogen bonds : angle 5.72537 / 3.87 ( 3105) Misc. bond : bond 0.00098 / 0.05 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 588 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 212 MET cc_start: 0.7321 (mmm) cc_final: 0.6570 (mtp) REVERT: 2 263 THR cc_start: 0.4909 (p) cc_final: 0.4705 (p) REVERT: 2 271 SER cc_start: 0.6422 (OUTLIER) cc_final: 0.6102 (t) REVERT: 2 290 LEU cc_start: 0.2641 (OUTLIER) cc_final: 0.2163 (mt) REVERT: 2 364 GLN cc_start: 0.5145 (OUTLIER) cc_final: 0.4938 (tt0) REVERT: 2 461 ARG cc_start: 0.6948 (ttp-110) cc_final: 0.6129 (ttp80) REVERT: 2 466 MET cc_start: 0.0870 (ttm) cc_final: 0.0265 (ttm) REVERT: 2 488 GLU cc_start: 0.5896 (mm-30) cc_final: 0.5225 (mm-30) REVERT: 2 587 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.6151 (tm-30) REVERT: 2 605 LEU cc_start: 0.6612 (tp) cc_final: 0.6032 (tp) REVERT: 2 720 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7686 (tt) REVERT: 2 727 LEU cc_start: 0.3310 (tt) cc_final: 0.2936 (mp) REVERT: 2 752 GLU cc_start: 0.5782 (pt0) cc_final: 0.4959 (pt0) REVERT: 2 791 MET cc_start: 0.4786 (mmt) cc_final: 0.4568 (mmt) REVERT: 3 65 ASN cc_start: 0.6022 (t0) cc_final: 0.5453 (t0) REVERT: 3 91 MET cc_start: 0.7532 (mpp) cc_final: 0.6716 (mpp) REVERT: 3 155 LYS cc_start: 0.6169 (tptt) cc_final: 0.5730 (tttt) REVERT: 3 253 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.5991 (t80) REVERT: 3 462 GLU cc_start: 0.6945 (tp30) cc_final: 0.6448 (tp30) REVERT: 3 604 THR cc_start: 0.3586 (OUTLIER) cc_final: 0.3315 (m) REVERT: 4 173 MET cc_start: 0.6762 (mmm) cc_final: 0.6518 (mmp) REVERT: 4 189 ILE cc_start: 0.1401 (OUTLIER) cc_final: 0.1027 (tt) REVERT: 4 649 ILE cc_start: 0.4724 (pt) cc_final: 0.4478 (pt) REVERT: 4 676 ARG cc_start: 0.2620 (pmt-80) cc_final: 0.1736 (ptm160) REVERT: 4 680 GLU cc_start: 0.2265 (OUTLIER) cc_final: 0.1139 (mt-10) REVERT: 5 210 MET cc_start: 0.6785 (mmp) cc_final: 0.5915 (mmp) REVERT: 5 220 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6765 (tt0) REVERT: 5 245 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6699 (t0) REVERT: 5 307 ARG cc_start: 0.5282 (OUTLIER) cc_final: 0.4933 (pmt170) REVERT: 5 417 LYS cc_start: 0.7606 (mptt) cc_final: 0.7364 (mttt) REVERT: 5 558 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.5292 (t80) REVERT: 5 562 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7752 (mp) REVERT: 6 161 ASN cc_start: 0.5064 (p0) cc_final: 0.4366 (m-40) REVERT: 6 284 LEU cc_start: 0.3732 (OUTLIER) cc_final: 0.3090 (pp) REVERT: 6 291 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6513 (tt) REVERT: 6 309 MET cc_start: 0.2643 (mtp) cc_final: 0.0719 (tmm) REVERT: 6 410 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.4001 (t80) REVERT: 7 57 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6150 (tp30) REVERT: 7 210 ASP cc_start: 0.5554 (t0) cc_final: 0.4469 (m-30) REVERT: 7 215 LYS cc_start: 0.1816 (OUTLIER) cc_final: 0.0847 (mtpt) REVERT: 7 281 MET cc_start: 0.6587 (mtm) cc_final: 0.6183 (mtp) REVERT: 7 299 GLN cc_start: 0.7213 (tp40) cc_final: 0.6574 (tt0) REVERT: 7 369 MET cc_start: 0.4082 (ptm) cc_final: 0.3596 (ptt) REVERT: 7 419 MET cc_start: -0.1515 (ttp) cc_final: -0.3853 (mmt) REVERT: 7 494 ARG cc_start: 0.4565 (ptm-80) cc_final: 0.3405 (ttm170) REVERT: A 53 MET cc_start: 0.5195 (mpp) cc_final: 0.4500 (mtm) REVERT: A 217 MET cc_start: 0.7353 (pmm) cc_final: 0.7086 (pmm) REVERT: A 398 GLU cc_start: 0.5872 (tt0) cc_final: 0.5608 (tt0) REVERT: A 507 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.5855 (mp) REVERT: L 120 ILE cc_start: 0.8307 (tp) cc_final: 0.7695 (mm) REVERT: M 84 VAL cc_start: 0.7158 (m) cc_final: 0.6939 (p) REVERT: M 108 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5781 (tt) outliers start: 204 outliers final: 157 residues processed: 741 average time/residue: 0.2495 time to fit residues: 306.2535 Evaluate side-chains 747 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 569 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 217 VAL Chi-restraints excluded: chain 2 residue 239 GLN Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 364 GLN Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 397 LEU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 404 THR Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 568 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 587 GLU Chi-restraints excluded: chain 2 residue 611 VAL Chi-restraints excluded: chain 2 residue 715 ILE Chi-restraints excluded: chain 2 residue 720 ILE Chi-restraints excluded: chain 2 residue 744 ILE Chi-restraints excluded: chain 2 residue 787 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 57 GLN Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 100 GLU Chi-restraints excluded: chain 3 residue 116 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 156 TYR Chi-restraints excluded: chain 3 residue 210 LEU Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 234 ILE Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 417 ILE Chi-restraints excluded: chain 3 residue 418 HIS Chi-restraints excluded: chain 3 residue 531 GLU Chi-restraints excluded: chain 3 residue 567 HIS Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 604 THR Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 189 ILE Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 230 ILE Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 570 ASN Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 646 PHE Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 208 PHE Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 481 VAL Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 69 LEU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 106 VAL Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 327 HIS Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 382 ILE Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 555 VAL Chi-restraints excluded: chain 6 residue 565 LEU Chi-restraints excluded: chain 6 residue 584 HIS Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 42 HIS Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 57 GLU Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 340 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 551 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 160 MET Chi-restraints excluded: chain N residue 194 VAL Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 205 optimal weight: 0.5980 chunk 263 optimal weight: 4.9990 chunk 348 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 432 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 211 ASN 2 586 HIS 2 592 GLN ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 584 HIS ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5120 r_free = 0.5120 target = 0.268108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.252798 restraints weight = 73854.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.252330 restraints weight = 107666.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.253245 restraints weight = 91307.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.253292 restraints weight = 73492.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.253544 restraints weight = 65818.816| |-----------------------------------------------------------------------------| r_work (final): 0.4992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5566 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 41741 Z= 0.161 Angle : 0.805 12.379 56508 Z= 0.403 Chirality : 0.047 0.305 6362 Planarity : 0.005 0.073 7230 Dihedral : 10.978 133.950 5929 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.22 % Favored : 86.76 % Rotamer: Outliers : 4.42 % Allowed : 27.68 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.11), residues: 5000 helix: -0.90 (0.13), residues: 1655 sheet: -2.69 (0.20), residues: 560 loop : -3.18 (0.11), residues: 2785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG 4 531 TYR 0.025 0.002 TYR M 107 PHE 0.028 0.002 PHE 2 282 TRP 0.029 0.002 TRP A 223 HIS 0.017 0.002 HIS 6 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (41733) covalent geometry : angle 0.80515 / 0.40 (56502) SS BOND : bond 0.00236 / 0.12 ( 3) SS BOND : angle 0.88923 / 0.46 ( 6) hydrogen bonds : bond 0.04376 / 2.87 ( 1089) hydrogen bonds : angle 5.71634 / 3.86 ( 3105) Misc. bond : bond 0.00118 / 0.06 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8018.55 seconds wall clock time: 139 minutes 56.69 seconds (8396.69 seconds total)